Skip to main content

Pangenome (pggb)

2 videos in this tutorial

JBrowse v5 beta

The tutorials target the JBrowse v5 beta, and the v4.3.0 release on the download page lacks some of what they show. To install the beta of JBrowse Web, run npm install -g @jbrowse/cli@next, then jbrowse create jbrowse2 --branch v5.0.0-beta.9. Desktop beta builds are coming soon.

We build a five-strain E. coli pangenome graph with pggb, then load what it produces in JBrowse: the graph's linear projections as ordinary tracks on the K12 genome, and the graph itself as a track you browse by locus. We:

  • run pggb over five RefSeq genomes to build the graph
  • draw its synteny, pangenome variants, whole-genome alignment and depth projections on K12's coordinates
  • browse the graph itself in the graph genome view, and jump from one of its segments into the strain that carries it
Experimental

The graph view is a beta plugin, and this tutorial covers experimental ideas. We welcome your feedback.

Prerequisites

  • docker or singularity, for the pggb image
  • samtools
  • bedGraphToBigWig (UCSC kentUtils)
  • python3
  • htslib (bgzip, tabix)
  • node, for the JBrowse CLI
  • the NCBI datasets CLI
  • unzip
  • the GraphGenomeView plugin, for the graph itself

On Debian/Ubuntu, apt install samtools tabix unzip python3 covers four of those. Docker installs from docs.docker.com; the NCBI datasets CLI and bedGraphToBigWig are each a single-binary download; and node comes from nodejs.org.

Where the data comes from

Five E. coli RefSeq assemblies, fetched by accession with the NCBI datasets CLI and concatenated into one PanSN-named FASTA for pggb.

The linear projections

A pangenome graph collapses many genomes into one structure. Shared sequence is a single path every sample walks, and the path branches where samples differ. pggb, Minigraph-Cactus and progressiveCactus build these graphs, and odgi manipulates them.

The graph's linear projections flatten it onto one reference genome's coordinates. Every builder emits them:

ProjectionWhat it showsFrom the graphJBrowse track
SyntenyThe blocks each pair of genomes sharesodgi untangle, halSyntenysynteny track
Pangenome variantsEvery difference the graph calls, across all samplespggb -V, cactus-pangenome --vcf, vg deconstructmulti-sample variant track
Whole-genome alignmentThe multiple alignment, column by columnpggb -M, hal2mafUser guide: MAF track
Pangenome depthHow many genomes cover each reference base (core/accessory)odgi depth, odgi pavquantitative track

Building the graph with pggb

pggb takes one FASTA of all the genomes, PanSN-named sample#haplotype#contig. Concatenate the five strains (haplotype 1, these being haploid) and index the result, chromosomes only:

for strain in K12 Sakai CFT073 NCTC86 IAI39; do
  awk -v s="$strain" '/^>/{print ">" s "#1#chr"; next} {print}' "$strain.fa"
done > all.fa
bgzip all.fa
samtools faidx all.fa.gz

The image pins all five tools at once and carries odgi, so wrap the docker run once. -V K12:10000 decomposes the graph into a VCF against the K12 path, and -M writes the MAF:

in_pggb() {
  docker run --rm -u "$(id -u):$(id -g)" -w /data -v "$PWD":/data \
    ghcr.io/pangenome/pggb:202603141454453ade6b "$@"
}

in_pggb pggb -i /data/all.fa.gz -o /data/pggb \
  -n 5 -c 4 -p 90 -s 5000 -V K12:10000 -M -t "$(nproc)"

-n is the number of haplotypes, -p the minimum alignment identity and -s the segment length; -p 90 -s 5000 suits a bacterial pangenome, and -c (mappings kept per segment) should rise alongside -n. Under singularity, singularity exec --bind "$PWD":/data --pwd /data docker://<image> replaces the wrapper body.

Resolve the graph's two spellings once, since the glob has to expand on the host:

gfa=$(ls pggb/*.smooth.final.gfa)
og=$(ls pggb/*.smooth.final.og)

Synteny projection

Two files answer this, a track each.

The alignment the graph was induced from

pggb's first step is a wfmash all-vs-all PAF, the same input the all-vs-all synteny tutorial loads. Index it with jbrowse make-pif and load it with an MultiGenomeIndexedPAFAdapter:

cp pggb/*.alignments.wfmash.paf ecoli_pggb_ava.paf
jbrowse make-pif ecoli_pggb_ava.paf   # -> ecoli_pggb_ava.pif.gz (+ .tbi)

Goes in the tracks array of config.json. See Tracks.

{
  "type": "SyntenyTrack",
  "trackId": "ecoli_pggb_ava",
  "name": "pggb graph: all-vs-all synteny (wfmash)",
  "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"],
  "adapter": {
    "type": "MultiGenomeIndexedPAFAdapter",
    "uri": "ecoli_pggb_ava.pif.gz",
    "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"]
  }
}
jbrowse add-track ecoli_pggb_ava.pif.gz \
  --trackId ecoli_pggb_ava \
  --name "pggb graph: all-vs-all synteny (wfmash)" \
  --assemblyNames K12,Sakai,CFT073,NCTC86,IAI39 \
  --adapterType MultiGenomeIndexedPAFAdapter \
  --load copy

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "SyntenyTrack",
  "trackId": "ecoli_pggb_ava",
  "name": "pggb graph: all-vs-all synteny (wfmash)",
  "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"],
  "adapter": {
    "type": "MultiGenomeIndexedPAFAdapter",
    "uri": "ecoli_pggb_ava.pif.gz",
    "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"]
  }
}

ecoli_pggb_ava.pif.gz is relative to a config.json. Replace it with its URL or its path on this computer.

That shows it in the linear view. For the synteny view, open Add → Linear synteny view, pick the track under Quick start, and click Launch.

Stack the five strains in a linear synteny view as the all-vs-all tutorial describes; the PanSN sample# prefix maps each record to its strain.

The wfmash alignment pggb induced the graph from: five strains stacked K12 to IAI39, a ribbon between each adjacent pair. The crossings in the bottom band are IAI39's inversions. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session.

Nothing happens?

Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearSyntenyView%22%2C%22views%22%3A%5B%7B%22assembly%22%3A%22K12%22%7D%2C%7B%22assembly%22%3A%22Sakai%22%7D%2C%7B%22assembly%22%3A%22CFT073%22%7D%2C%7B%22assembly%22%3A%22NCTC86%22%7D%2C%7B%22assembly%22%3A%22IAI39%22%7D%5D%2C%22tracks%22%3A%5B%5B%22ecoli_pggb_ava%22%5D%2C%5B%22ecoli_pggb_ava%22%5D%2C%5B%22ecoli_pggb_ava%22%5D%2C%5B%22ecoli_pggb_ava%22%5D%5D%2C%22drawCurves%22%3Afalse%2C%22minAlignmentLength%22%3A10000%2C%22levelHeights%22%3A%5B110%2C110%2C110%2C110%5D%2C%22collapseEmptyRows%22%3Atrue%7D%5D%7D&sessionName=JBrowse+docs%3A+pangenome%2Fpggb_synteny

With your own data, the steps behind the figure:

  1. Open your genomes: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one), then File → Open genome... for each of the rest.This figure's rows, top to bottom: K12, Sakai, CFT073, NCTC86, IAI39.
  2. Open the view: Add → Linear synteny view, and set the rows to those assemblies in the import form.
  3. Point the import form at your own file: click the arrow between two rows, choose New track, and paste a URL or pick a local file.A synteny track the session already has is quicker: pick it under Quick start, which fills in the rows itself.This figure uses “pggb graph: all-vs-all synteny (wfmash)” for all 4 bands.
  4. Click Launch.
  5. Synteny display settings (the sliders button in the view header) → Curved lines (unchecked)
  6. Synteny display settings (the sliders button in the view header) → Min length → drag to 10,000bpHides alignments shorter than this, which is what clears the hairball of short spurious chains at whole-genome zoom.
  7. Drag the bar below a synteny level to resize it.This figure's 4 levels are 110, 110, 110, 110px tall.

Open this view in JBrowse Web ↗

Its genome and tracks are hosted, so File → Open track... there adds your own files beside them.

With your own data, the steps behind the figure:

  1. Put your genomes in your JBrowse Web's config.json: run jbrowse add-assembly once for each.This figure's rows, top to bottom: K12, Sakai, CFT073, NCTC86, IAI39.
  2. Open the view: Add → Linear synteny view, and set the rows to those assemblies in the import form.
  3. Point the import form at your own file: click the arrow between two rows, choose New track, and paste a URL or pick a local file.A synteny track the session already has is quicker: pick it under Quick start, which fills in the rows itself.This figure uses “pggb graph: all-vs-all synteny (wfmash)” for all 4 bands.
  4. Click Launch.
  5. Synteny display settings (the sliders button in the view header) → Curved lines (unchecked)
  6. Synteny display settings (the sliders button in the view header) → Min length → drag to 10,000bpHides alignments shorter than this, which is what clears the hairball of short spurious chains at whole-genome zoom.
  7. Drag the bar below a synteny level to resize it.This figure's 4 levels are 110, 110, 110, 110px tall.

This session spec draws the figure from https://jbrowse.org/demos/ecoli_pangenome/config.json: paste it after &session=spec- on a JBrowse Web link that loads that config.

{
  "views": [
    {
      "type": "LinearSyntenyView",
      "views": [
        {
          "assembly": "K12"
        },
        {
          "assembly": "Sakai"
        },
        {
          "assembly": "CFT073"
        },
        {
          "assembly": "NCTC86"
        },
        {
          "assembly": "IAI39"
        }
      ],
      "tracks": [
        [
          "ecoli_pggb_ava"
        ],
        [
          "ecoli_pggb_ava"
        ],
        [
          "ecoli_pggb_ava"
        ],
        [
          "ecoli_pggb_ava"
        ]
      ],
      "drawCurves": false,
      "minAlignmentLength": 10000,
      "levelHeights": [
        110,
        110,
        110,
        110
      ],
      "collapseEmptyRows": true
    }
  ]
}

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/demos/ecoli_pangenome/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearSyntenyView",
            "views": [
                {
                    "assembly": "K12"
                },
                {
                    "assembly": "Sakai"
                },
                {
                    "assembly": "CFT073"
                },
                {
                    "assembly": "NCTC86"
                },
                {
                    "assembly": "IAI39"
                }
            ],
            "tracks": [
                [
                    "ecoli_pggb_ava"
                ],
                [
                    "ecoli_pggb_ava"
                ],
                [
                    "ecoli_pggb_ava"
                ],
                [
                    "ecoli_pggb_ava"
                ]
            ],
            "drawCurves": False,
            "minAlignmentLength": 10000,
            "levelHeights": [
                110,
                110,
                110,
                110
            ],
            "collapseEmptyRows": True
        }
    ],
)
app  # display the widget

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file with --bam, --vcfgz and the other file flags.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearSyntenyView",
      "views": [
        {
          "assembly": "K12"
        },
        {
          "assembly": "Sakai"
        },
        {
          "assembly": "CFT073"
        },
        {
          "assembly": "NCTC86"
        },
        {
          "assembly": "IAI39"
        }
      ],
      "tracks": [
        [
          "ecoli_pggb_ava"
        ],
        [
          "ecoli_pggb_ava"
        ],
        [
          "ecoli_pggb_ava"
        ],
        [
          "ecoli_pggb_ava"
        ]
      ],
      "drawCurves": false,
      "minAlignmentLength": 10000,
      "levelHeights": [
        110,
        110,
        110,
        110
      ],
      "collapseEmptyRows": true
    }
  ]
}
JSON

npx @jbrowse/img synteny --config https://jbrowse.org/demos/ecoli_pangenome/config.json \
  --spec session.json \
  --width 1500 --out figure.svg

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearSyntenyView",
      "views": [
        {
          "assembly": "K12"
        },
        {
          "assembly": "Sakai"
        },
        {
          "assembly": "CFT073"
        },
        {
          "assembly": "NCTC86"
        },
        {
          "assembly": "IAI39"
        }
      ],
      "tracks": [
        [
          "ecoli_pggb_ava"
        ],
        [
          "ecoli_pggb_ava"
        ],
        [
          "ecoli_pggb_ava"
        ],
        [
          "ecoli_pggb_ava"
        ]
      ],
      "drawCurves": false,
      "minAlignmentLength": 10000,
      "levelHeights": [
        110,
        110,
        110,
        110
      ],
      "collapseEmptyRows": true
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/ecoli_pangenome/config.json \
  --width 1500 --height 715 \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

The projection from odgi untangle

odgi untangle walks each query path and reports which stretch of the reference path it traverses, so it reads homology the way the graph resolved it:

printf 'K12#1#chr\n' > target.txt
printf 'Sakai#1#chr\nCFT073#1#chr\nNCTC86#1#chr\nIAI39#1#chr\n' > query.txt
# -m merges short runs into the previous segment; -j is the minimum jaccard
# -e forces a boundary every N bp; omit it on graphs with many haplotypes
# -p asks for PAF, so make-pif reads it directly
in_pggb odgi untangle -i "/data/$og" \
  -R /data/target.txt -Q /data/query.txt -m 1000 -j 0.5 -e 5000 -p -t "$(nproc)" \
  > ecoli_pggb_untangle.paf
jbrowse make-pif ecoli_pggb_untangle.paf

Load it as a separate SyntenyTrack:

Goes in the tracks array of config.json. See Tracks.

{
  "type": "SyntenyTrack",
  "trackId": "ecoli_pggb_untangle",
  "name": "pggb graph: synteny from the graph (odgi untangle)",
  "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"],
  "adapter": {
    "type": "MultiGenomeIndexedPAFAdapter",
    "uri": "ecoli_pggb_untangle.pif.gz",
    "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"]
  }
}
jbrowse add-track ecoli_pggb_untangle.pif.gz \
  --trackId ecoli_pggb_untangle \
  --name "pggb graph: synteny from the graph (odgi untangle)" \
  --assemblyNames K12,Sakai,CFT073,NCTC86,IAI39 \
  --adapterType MultiGenomeIndexedPAFAdapter \
  --load copy

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "SyntenyTrack",
  "trackId": "ecoli_pggb_untangle",
  "name": "pggb graph: synteny from the graph (odgi untangle)",
  "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"],
  "adapter": {
    "type": "MultiGenomeIndexedPAFAdapter",
    "uri": "ecoli_pggb_untangle.pif.gz",
    "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"]
  }
}

ecoli_pggb_untangle.pif.gz is relative to a config.json. Replace it with its URL or its path on this computer.

That shows it in the linear view. For the synteny view, open Add → Linear synteny view, pick the track under Quick start, and click Launch.

Put the reference between the strains you want to compare.

The wfmash alignment and the untangle projection differ at a repeat, a reference span more than one segment of the same query lands on:

gzip -dc ecoli_pggb_untangle.pif.gz | awk -F'\t' 'substr($1,1,1)=="q"' \
  | cut -f1,3,4,8,9 | sort -k4,4n

Two K12 spans come back where Sakai, NCTC86 and IAI39 land twice and CFT073 once, a repeat a pairwise PAF collapses to one.

One lane per strain, on the K12 axis

The untangle PAF, drawn as a multi-row feature track, puts every strain on the reference at once, orientation read down each row.

untangle_to_bed.py projects the PAF onto the per-strain BED schema build_minigraph_paths.sh defines, so rows and the colors carry across:

curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/untangle_to_bed.py
python3 untangle_to_bed.py ecoli_pggb_untangle.paf chr > ecoli_pggb_untangle_rows.bed
# the header line is `#`-prefixed; sort-bed keeps it on top (sort -k1,1 -k2,2n)
jbrowse sort-bed ecoli_pggb_untangle_rows.bed | bgzip > ecoli_pggb_untangle_rows.bed.gz
tabix -p bed ecoli_pggb_untangle_rows.bed.gz

Load the result as a FeatureTrack with a LinearMultiRowFeatureDisplay:

Goes in the tracks array of config.json. See Tracks.

{
  "type": "FeatureTrack",
  "trackId": "ecoli_pggb_untangle_rows",
  "name": "pggb graph: untangle per strain (orientation, vs K12)",
  "assemblyNames": ["K12"],
  "adapter": {
    "type": "BedTabixAdapter",
    "uri": "ecoli_pggb_untangle_rows.bed.gz"
  },
  "displays": [
    {
      "type": "LinearMultiRowFeatureDisplay",
      "rows": {
        "field": "strain",
        "domain": ["Sakai", "CFT073", "NCTC86", "IAI39"]
      },
      "color": {
        "scale": "identity",
        "domain": ["rgb(153,153,153)", "rgb(214,39,40)"],
        "labels": ["Same orientation as K12", "Inverted"]
      }
    }
  ]
}
jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "ecoli_pggb_untangle_rows",
  "name": "pggb graph: untangle per strain (orientation, vs K12)",
  "assemblyNames": ["K12"],
  "adapter": {
    "type": "BedTabixAdapter",
    "uri": "ecoli_pggb_untangle_rows.bed.gz"
  },
  "displays": [
    {
      "type": "LinearMultiRowFeatureDisplay",
      "rows": {
        "field": "strain",
        "domain": ["Sakai", "CFT073", "NCTC86", "IAI39"]
      },
      "color": {
        "scale": "identity",
        "domain": ["rgb(153,153,153)", "rgb(214,39,40)"],
        "labels": ["Same orientation as K12", "Inverted"]
      }
    }
  ]
}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "FeatureTrack",
  "trackId": "ecoli_pggb_untangle_rows",
  "name": "pggb graph: untangle per strain (orientation, vs K12)",
  "assemblyNames": ["K12"],
  "adapter": {
    "type": "BedTabixAdapter",
    "uri": "ecoli_pggb_untangle_rows.bed.gz"
  },
  "displays": [
    {
      "type": "LinearMultiRowFeatureDisplay",
      "rows": {
        "field": "strain",
        "domain": ["Sakai", "CFT073", "NCTC86", "IAI39"]
      },
      "color": {
        "scale": "identity",
        "domain": ["rgb(153,153,153)", "rgb(214,39,40)"],
        "labels": ["Same orientation as K12", "Inverted"]
      }
    }
  ]
}

ecoli_pggb_untangle_rows.bed.gz is relative to a config.json. Replace it with its URL or its path on this computer.

The untangle projection read two ways, with each of IAI39's five inverted arms boxed in a distinct color in both. Above, one row per strain over the whole K12 chromosome, red where the strain runs backwards and white where it has no segment at all; only IAI39 is inverted at length. Below, K12 against IAI39 as a dotplot, where every descending segment is an inversion. Open in JBrowse: Rows ↗ · Dotplot ↗ (large dataset — this session takes a while to load)

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session.

Nothing happens?

Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22K12%22%2C%22loc%22%3A%22chr%3A1-4%2C641%2C652%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22ecoli_pggb_untangle_rows%22%2C%22type%22%3A%22LinearMultiRowFeatureDisplay%22%2C%22height%22%3A240%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+pangenome%2Fpggb_untangle_rows

With your own data, the steps behind the figure:

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed BED (.bed.gz + .tbi).This figure uses “pggb graph: untangle per strain (orientation, vs K12)”.
    1. Drag the bar at the bottom edge of the track to resize it (240px here).
  3. Type your region of interest into the location box and press Enter.This figure is at chr:1-4,641,652.

Open this view in JBrowse Web ↗

Its genome and tracks are hosted, so File → Open track... there adds your own files beside them.

With your own data, the steps behind the figure:

  1. Put your genome in your JBrowse Web's config.json: jbrowse add-assembly adds it.This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed BED (.bed.gz + .tbi).This figure uses “pggb graph: untangle per strain (orientation, vs K12)”.
    1. Drag the bar at the bottom edge of the track to resize it (240px here).
  3. Type your region of interest into the location box and press Enter.This figure is at chr:1-4,641,652.

This session spec draws the figure from https://jbrowse.org/demos/ecoli_pangenome/config.json: paste it after &session=spec- on a JBrowse Web link that loads that config.

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:1-4,641,652",
      "tracks": [
        {
          "trackId": "ecoli_pggb_untangle_rows",
          "type": "LinearMultiRowFeatureDisplay",
          "height": 240
        }
      ]
    }
  ]
}

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/demos/ecoli_pangenome/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "K12",
            "loc": "chr:1-4,641,652",
            "tracks": [
                {
                    "trackId": "ecoli_pggb_untangle_rows",
                    "type": "LinearMultiRowFeatureDisplay",
                    "height": 240
                }
            ]
        }
    ],
)
app  # display the widget

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file with --bam, --vcfgz and the other file flags.

npx @jbrowse/img --config https://jbrowse.org/demos/ecoli_pangenome/config.json \
  --assembly K12 --loc chr:1-4,641,652 \
  --track ecoli_pggb_untangle_rows display:LinearMultiRowFeatureDisplay '{"height":240}' \
  --width 1000 --out figure.svg

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:1-4,641,652",
      "tracks": [
        {
          "trackId": "ecoli_pggb_untangle_rows",
          "type": "LinearMultiRowFeatureDisplay",
          "height": 240
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/ecoli_pangenome/config.json \
  --width 1000 --height 450 \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session.

Nothing happens?

Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22DotplotView%22%2C%22tracks%22%3A%5B%22ecoli_pggb_untangle%22%5D%2C%22views%22%3A%5B%7B%22assembly%22%3A%22K12%22%7D%2C%7B%22assembly%22%3A%22IAI39%22%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+pangenome%2Fpggb_untangle_dotplot

With your own data, the steps behind the figure:

  1. Open your genomes: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one), then File → Open genome... for each of the rest.This figure has K12 on X and IAI39 on Y.
  2. Open the view: Add → Dotplot view, and set both axes to those assemblies in the import form.
  3. Point the import form at your own file: use the track panel under the two axis selectors, choose New track, and paste a URL or pick a local file.A synteny track the session already has is quicker: pick it under Quick start, which fills in both axes itself.This figure uses “pggb graph: synteny from the graph (odgi untangle)”.
  4. Click Launch.

Open this view in JBrowse Web ↗

Its genome and tracks are hosted, so File → Open track... there adds your own files beside them.

With your own data, the steps behind the figure:

  1. Put your genomes in your JBrowse Web's config.json: run jbrowse add-assembly once for each.This figure has K12 on X and IAI39 on Y.
  2. Open the view: Add → Dotplot view, and set both axes to those assemblies in the import form.
  3. Point the import form at your own file: use the track panel under the two axis selectors, choose New track, and paste a URL or pick a local file.A synteny track the session already has is quicker: pick it under Quick start, which fills in both axes itself.This figure uses “pggb graph: synteny from the graph (odgi untangle)”.
  4. Click Launch.

This session spec draws the figure from https://jbrowse.org/demos/ecoli_pangenome/config.json: paste it after &session=spec- on a JBrowse Web link that loads that config.

{
  "views": [
    {
      "type": "DotplotView",
      "tracks": [
        "ecoli_pggb_untangle"
      ],
      "views": [
        {
          "assembly": "K12"
        },
        {
          "assembly": "IAI39"
        }
      ]
    }
  ]
}

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/demos/ecoli_pangenome/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "DotplotView",
            "tracks": [
                "ecoli_pggb_untangle"
            ],
            "views": [
                {
                    "assembly": "K12"
                },
                {
                    "assembly": "IAI39"
                }
            ]
        }
    ],
)
app  # display the widget

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file with --bam, --vcfgz and the other file flags.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "DotplotView",
      "tracks": [
        "ecoli_pggb_untangle"
      ],
      "views": [
        {
          "assembly": "K12"
        },
        {
          "assembly": "IAI39"
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/img dotplot --config https://jbrowse.org/demos/ecoli_pangenome/config.json \
  --spec session.json \
  --width 1000 --out figure.svg

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "DotplotView",
      "tracks": [
        "ecoli_pggb_untangle"
      ],
      "views": [
        {
          "assembly": "K12"
        },
        {
          "assembly": "IAI39"
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/ecoli_pangenome/config.json \
  --width 1000 --height 640 \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

selfCov in the popup goes above 1 where a segment repeats within the same strain; jexl:feature.selfCov>1 in Edit filters cuts the lane to those repeats.

Pangenome variants projection

pggb -V writes a VCF of every variant the graph decomposes against the K12 path, genotyped across the other four strains. Its CHROM is the PanSN path (K12#1#chr), so rename it to the assembly's refName (chr) with bcftools:

printf 'K12#1#chr\tchr\n' > rename_chrs.tsv
in_pggb bash -c "bcftools annotate --rename-chrs /data/rename_chrs.tsv \
  /data/pggb/*.smooth.final.K12.decomposed.vcf \
  | bcftools sort -Oz -o /data/ecoli_pggb.vcf.gz && tabix -p vcf /data/ecoli_pggb.vcf.gz"

Load it as a VariantTrack on K12 with the multi-sample display, one row per sample:

Goes in the tracks array of config.json. See Tracks.

{
  "type": "VariantTrack",
  "trackId": "ecoli_pggb_variants",
  "name": "pggb graph: pangenome variants (vs K12)",
  "assemblyNames": ["K12"],
  "adapter": {
    "type": "VcfTabixAdapter",
    "uri": "ecoli_pggb.vcf.gz"
  },
  "displays": [{ "type": "LinearMultiSampleVariantDisplay" }]
}
jbrowse add-track-json '{
  "type": "VariantTrack",
  "trackId": "ecoli_pggb_variants",
  "name": "pggb graph: pangenome variants (vs K12)",
  "assemblyNames": ["K12"],
  "adapter": {
    "type": "VcfTabixAdapter",
    "uri": "ecoli_pggb.vcf.gz"
  },
  "displays": [{ "type": "LinearMultiSampleVariantDisplay" }]
}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "VariantTrack",
  "trackId": "ecoli_pggb_variants",
  "name": "pggb graph: pangenome variants (vs K12)",
  "assemblyNames": ["K12"],
  "adapter": {
    "type": "VcfTabixAdapter",
    "uri": "ecoli_pggb.vcf.gz"
  },
  "displays": [{ "type": "LinearMultiSampleVariantDisplay" }]
}

ecoli_pggb.vcf.gz is relative to a config.json. Replace it with its URL or its path on this computer.

The variant calls, stacked over the MAF alignment, sit over the alignment they were decomposed from.

Why the reference path takes a length

With a length, pggb runs vcfbub -l 0 -a LEN piped into vcfwave, decomposing any site whose alleles run past LEN into the primitive variants *.decomposed.vcf carries.

Keep the raw file, similarly renamed, as a second track:

in_pggb bash -c "bcftools annotate --rename-chrs /data/rename_chrs.tsv \
  /data/pggb/*.smooth.final.K12.vcf \
  | bcftools sort -Oz -o /data/ecoli_pggb_snarls.vcf.gz && tabix -p vcf /data/ecoli_pggb_snarls.vcf.gz"

LV/PS give the snarl tree. Filter on LV in Edit filters to pick one level. The coarse tier below is built from the LV=0 records.

Whole-genome alignment (MAF) projection

pggb -M writes the multiple alignment as a MAF, read as a Config guide: MAF track. Its blocks are smoothxg's POA blocks, with two consequences.

Block order. Re-root every block on K12, drop blocks that lack it, and rename the PanSN names to sample.chr:

curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/reroot_maf.py
# keeps K12-containing blocks, puts K12 first, sorts by K12 position, and
# splits a repeat-collapsed block's second K12 row into its own block
python3 reroot_maf.py pggb/*.smooth.maf ecoli_pggb.maf K12#1#chr

Block padding. A smoothxg bug leaves block padding on some rows; reroot_maf.py crops around it.

Then convert the MAF to the tabix-indexed BED the MafTabixAdapter reads, with maf_to_bed.py, which takes row 0 as the reference:

curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/maf_to_bed.py
python3 maf_to_bed.py ecoli_pggb.maf ecoli_pggb.maf.bed
bgzip ecoli_pggb.maf.bed
tabix -p bed ecoli_pggb.maf.bed.gz

For row order, odgi similarity reports how much of the graph each pair shares; UPGMA over 1 - estimated.identity gives the Newick read as nhLocation:

curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/odgi_similarity_to_newick.py
in_pggb odgi similarity -i "/data/$og" -D '#' -p 1 > ecoli_pggb_similarity.tsv
python3 odgi_similarity_to_newick.py ecoli_pggb_similarity.tsv ecoli_pggb.nh

Goes in the tracks array of config.json. See Tracks.

{
  "type": "MafTrack",
  "trackId": "ecoli_pggb_maf",
  "name": "pggb graph: whole-genome alignment (MAF, vs K12)",
  "assemblyNames": ["K12"],
  "adapter": {
    "type": "MafTabixAdapter",
    "samples": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"],
    "nhLocation": { "uri": "ecoli_pggb.nh" },
    "uri": "ecoli_pggb.maf.bed.gz"
  }
}
jbrowse add-track-json '{
  "type": "MafTrack",
  "trackId": "ecoli_pggb_maf",
  "name": "pggb graph: whole-genome alignment (MAF, vs K12)",
  "assemblyNames": ["K12"],
  "adapter": {
    "type": "MafTabixAdapter",
    "samples": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"],
    "nhLocation": { "uri": "ecoli_pggb.nh" },
    "uri": "ecoli_pggb.maf.bed.gz"
  }
}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "MafTrack",
  "trackId": "ecoli_pggb_maf",
  "name": "pggb graph: whole-genome alignment (MAF, vs K12)",
  "assemblyNames": ["K12"],
  "adapter": {
    "type": "MafTabixAdapter",
    "samples": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"],
    "nhLocation": { "uri": "ecoli_pggb.nh" },
    "uri": "ecoli_pggb.maf.bed.gz"
  }
}

ecoli_pggb.nh, ecoli_pggb.maf.bed.gz are relative to a config.json. Replace each with its URL or its path on this computer.

The graph's whole-genome alignment projected onto K12, one row per strain in the tree's order, with the variant calls above. A blank row is a strain with no alignment to K12 there. Open this view in JBrowse ↗

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session.

Nothing happens?

Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22K12%22%2C%22loc%22%3A%22chr%3A4%2C540%2C000-4%2C600%2C000%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22K12_genes%22%2C%22type%22%3A%22LinearBasicDisplay%22%7D%2C%7B%22trackId%22%3A%22ecoli_pggb_variants%22%2C%22type%22%3A%22LinearMultiSampleVariantDisplay%22%2C%22height%22%3A120%7D%2C%7B%22trackId%22%3A%22ecoli_pggb_maf%22%2C%22type%22%3A%22LinearMafDisplay%22%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+pangenome%2Fmaf

With your own data, the steps behind the figure:

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “K12 genes”.
  3. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed VCF (.vcf.gz + .tbi).This figure uses “pggb graph: pangenome variants (vs K12)”.
    1. Drag the bar at the bottom edge of the track to resize it (120px here).
  4. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed MAF (.maf.gz + .tbi).This figure uses “pggb graph: whole-genome alignment (MAF, vs K12)”.
  5. Type your region of interest into the location box and press Enter.This figure is at chr:4,540,000-4,600,000.

Open this view in JBrowse Web ↗

Its genome and tracks are hosted, so File → Open track... there adds your own files beside them.

With your own data, the steps behind the figure:

  1. Put your genome in your JBrowse Web's config.json: jbrowse add-assembly adds it.This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “K12 genes”.
  3. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed VCF (.vcf.gz + .tbi).This figure uses “pggb graph: pangenome variants (vs K12)”.
    1. Drag the bar at the bottom edge of the track to resize it (120px here).
  4. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed MAF (.maf.gz + .tbi).This figure uses “pggb graph: whole-genome alignment (MAF, vs K12)”.
  5. Type your region of interest into the location box and press Enter.This figure is at chr:4,540,000-4,600,000.

This session spec draws the figure from https://jbrowse.org/demos/ecoli_pangenome/config.json: paste it after &session=spec- on a JBrowse Web link that loads that config.

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:4,540,000-4,600,000",
      "tracks": [
        {
          "trackId": "K12_genes",
          "type": "LinearBasicDisplay"
        },
        {
          "trackId": "ecoli_pggb_variants",
          "type": "LinearMultiSampleVariantDisplay",
          "height": 120
        },
        {
          "trackId": "ecoli_pggb_maf",
          "type": "LinearMafDisplay"
        }
      ]
    }
  ]
}

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/demos/ecoli_pangenome/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "K12",
            "loc": "chr:4,540,000-4,600,000",
            "tracks": [
                {
                    "trackId": "K12_genes",
                    "type": "LinearBasicDisplay"
                },
                {
                    "trackId": "ecoli_pggb_variants",
                    "type": "LinearMultiSampleVariantDisplay",
                    "height": 120
                },
                {
                    "trackId": "ecoli_pggb_maf",
                    "type": "LinearMafDisplay"
                }
            ]
        }
    ],
)
app  # display the widget

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file with --bam, --vcfgz and the other file flags.

npx @jbrowse/img --config https://jbrowse.org/demos/ecoli_pangenome/config.json \
  --assembly K12 --loc chr:4,540,000-4,600,000 \
  --track K12_genes display:LinearBasicDisplay \
  --track ecoli_pggb_variants display:LinearMultiSampleVariantDisplay '{"height":120}' \
  --track ecoli_pggb_maf display:LinearMafDisplay \
  --width 1000 --out figure.svg

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:4,540,000-4,600,000",
      "tracks": [
        {
          "trackId": "K12_genes",
          "type": "LinearBasicDisplay"
        },
        {
          "trackId": "ecoli_pggb_variants",
          "type": "LinearMultiSampleVariantDisplay",
          "height": 120
        },
        {
          "trackId": "ecoli_pggb_maf",
          "type": "LinearMafDisplay"
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/ecoli_pangenome/config.json \
  --width 1000 --height 660 \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

The track colors each variant-lane cell by that strain's genotype:

  • grey where the strain matches K12
  • blue where it carries the alternate allele
  • olive where the site is uncalled
  • a numbered purple box for an insertion, the number giving its length in bases beyond K12

An insertion consumes no reference, so the record spans one base and the marker carries its length.

Drag across the rows and the menu that opens on release lists each strain the selection covers under two submenus:

  • Open aligned genome at the matching region opens that strain's own genome at the aligned stretch
  • Linear synteny view, K12 vs... opens the two as a linear synteny view
From the pggb alignment's rows to a two-strain synteny view: a drag across the rows, the menu listing the strains it covers, and the synteny view the NCTC86 entry opens, with K12's genes over the alignment and NCTC86's genes under the ribbon. Open the session this video starts in ↗

Open the session the video starts in ↗, then take the steps it shows:

  1. The alignment, one row per strain
  2. Drag across the rows
  3. One entry per strain the drag covers
  4. NCTC86
  5. K-12 over NCTC86, the ribbon cut from the columns

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session.

Nothing happens?

Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22K12%22%2C%22loc%22%3A%22chr%3A798%2C300-801%2C100%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22K12_genes%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22showOnlyGenes%22%3Atrue%2C%22displayMode%22%3A%22compact%22%7D%2C%7B%22trackId%22%3A%22ecoli_pggb_maf%22%2C%22type%22%3A%22LinearMafDisplay%22%2C%22showTree%22%3Atrue%2C%22height%22%3A150%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+synteny%2Fmaf_row_synteny

With your own data, the steps behind the figure:

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “K12 genes”.
    1. Track menu → Show only genes (checked)
    2. Track menu → Feature height → Compact
  3. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed MAF (.maf.gz + .tbi).This figure uses “pggb graph: whole-genome alignment (MAF, vs K12)”.
    1. Track menu → Show... → Show tree (checked)On by default. The item is disabled until there is a tree to show — a clustering run, or a MAF track’s guide tree; the row labels have their own toggle beneath it.
    2. Drag the bar at the bottom edge of the track to resize it (150px here).
  4. Type your region of interest into the location box and press Enter.This figure is at chr:798,300-801,100.

Open this view in JBrowse Web ↗

Its genome and tracks are hosted, so File → Open track... there adds your own files beside them.

With your own data, the steps behind the figure:

  1. Put your genome in your JBrowse Web's config.json: jbrowse add-assembly adds it.This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “K12 genes”.
    1. Track menu → Show only genes (checked)
    2. Track menu → Feature height → Compact
  3. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed MAF (.maf.gz + .tbi).This figure uses “pggb graph: whole-genome alignment (MAF, vs K12)”.
    1. Track menu → Show... → Show tree (checked)On by default. The item is disabled until there is a tree to show — a clustering run, or a MAF track’s guide tree; the row labels have their own toggle beneath it.
    2. Drag the bar at the bottom edge of the track to resize it (150px here).
  4. Type your region of interest into the location box and press Enter.This figure is at chr:798,300-801,100.

This session spec draws the figure from https://jbrowse.org/demos/ecoli_pangenome/config.json: paste it after &session=spec- on a JBrowse Web link that loads that config.

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:798,300-801,100",
      "tracks": [
        {
          "trackId": "K12_genes",
          "type": "LinearBasicDisplay",
          "showOnlyGenes": true,
          "displayMode": "compact"
        },
        {
          "trackId": "ecoli_pggb_maf",
          "type": "LinearMafDisplay",
          "showTree": true,
          "height": 150
        }
      ]
    }
  ]
}

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/demos/ecoli_pangenome/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "K12",
            "loc": "chr:798,300-801,100",
            "tracks": [
                {
                    "trackId": "K12_genes",
                    "type": "LinearBasicDisplay",
                    "showOnlyGenes": True,
                    "displayMode": "compact"
                },
                {
                    "trackId": "ecoli_pggb_maf",
                    "type": "LinearMafDisplay",
                    "showTree": True,
                    "height": 150
                }
            ]
        }
    ],
)
app  # display the widget

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file with --bam, --vcfgz and the other file flags.

npx @jbrowse/img --config https://jbrowse.org/demos/ecoli_pangenome/config.json \
  --assembly K12 --loc chr:798,300-801,100 \
  --track K12_genes display:LinearBasicDisplay '{"showOnlyGenes":true,"displayMode":"compact"}' \
  --track ecoli_pggb_maf display:LinearMafDisplay '{"showTree":true,"height":150}' \
  --width 1920 --out figure.svg

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:798,300-801,100",
      "tracks": [
        {
          "trackId": "K12_genes",
          "type": "LinearBasicDisplay",
          "showOnlyGenes": true,
          "displayMode": "compact"
        },
        {
          "trackId": "ecoli_pggb_maf",
          "type": "LinearMafDisplay",
          "showTree": true,
          "height": 150
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/ecoli_pangenome/config.json \
  --width 1920 --height 1260 \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

Pangenome depth projection (core vs accessory)

odgi depth counts how many paths traverse each reference base, near the strain count over core sequence and toward 1 over K12-private sequence:

reflen=$(awk -v p="K12#1#chr" '$1 == p {print $2}' all.fa.gz.fai)
awk -v p="K12#1#chr" -v len="$reflen" -v w=500 \
  'BEGIN { for (s = 0; s < len; s += w) { e = s + w; if (e > len) e = len
           print p "\t" s "\t" e } }' > depth_windows.bed

# -b gives one row per window, so window size sets the curve's resolution;
# the awk drops the PanSN prefix for K12's plain refName
in_pggb odgi depth -i "/data/$og" -b /data/depth_windows.bed |
  awk -v p="K12#1#chr" -v OFS='\t' '$1 == p && $4 + 0 == $4 { print "chr", $2, $3, $4 }' |
  sort -k1,1 -k2,2n > ecoli_pggb_depth.bedgraph

printf 'chr\t%s\n' "$reflen" > chrom.sizes
bedGraphToBigWig ecoli_pggb_depth.bedgraph chrom.sizes ecoli_pggb_depth.bw

chrom.sizes is written by hand, since the .fai carries the PanSN path.

Load it as a QuantitativeTrack on K12:

Goes in the tracks array of config.json. See Tracks.

{
  "type": "QuantitativeTrack",
  "trackId": "ecoli_pggb_depth",
  "name": "pggb graph: pangenome depth (paths over K12)",
  "assemblyNames": ["K12"],
  "adapter": {
    "type": "BigWigAdapter",
    "uri": "ecoli_pggb_depth.bw"
  }
}
jbrowse add-track ecoli_pggb_depth.bw \
  --trackId ecoli_pggb_depth \
  --name "pggb graph: pangenome depth (paths over K12)" \
  --assemblyNames K12 \
  --load copy

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "QuantitativeTrack",
  "trackId": "ecoli_pggb_depth",
  "name": "pggb graph: pangenome depth (paths over K12)",
  "assemblyNames": ["K12"],
  "adapter": {
    "type": "BigWigAdapter",
    "uri": "ecoli_pggb_depth.bw"
  }
}

ecoli_pggb_depth.bw is relative to a config.json. Replace it with its URL or its path on this computer.

Zoomed out, the track shows the pangenome's core/accessory landscape:

  • a plateau near the strain count
  • spikes past it over the rRNA operons the graph collapses into one copy
  • troughs at 1 over K12's private sequence

The depth lane is drawn at the end of this section, under the per-strain rows.

An unrelated isolate's long reads show the same thing without the graph: nanopore reads from E. coli E146, mapped straight onto K12 with minimap2 -ax map-ont. Reads long enough to cross the element carry it as a single labelled deletion.

Nanopore reads from an unrelated E. coli isolate over one K12 depth trough, with the graph's depth curve and its MAF below. All four lanes break at the edges of the cryptic prophage CPZ-55. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session.

Nothing happens?

Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22K12%22%2C%22loc%22%3A%22chr%3A2%2C554%2C000-2%2C570%2C000%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22K12_genes%22%2C%22type%22%3A%22LinearBasicDisplay%22%7D%2C%7B%22trackId%22%3A%22ecoli_e146_ont%22%2C%22type%22%3A%22LinearAlignmentsDisplay%22%2C%22linkedReads%22%3A%22normal%22%2C%22facet%22%3A%22splitRead%22%2C%22height%22%3A210%7D%2C%7B%22trackId%22%3A%22ecoli_pggb_depth%22%2C%22type%22%3A%22LinearWiggleDisplay%22%2C%22height%22%3A100%7D%2C%7B%22trackId%22%3A%22ecoli_pggb_maf%22%2C%22type%22%3A%22LinearMafDisplay%22%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+pangenome%2Flong_reads

With your own data, the steps behind the figure:

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “K12 genes”.
  3. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a BAM file (.bam + .bai).This figure uses “E146 nanopore reads (vs K12)”.
    1. Track menu → Read connections → View as pairs / link supplementary alignments (checked)
    2. Track menu → Group by... → Split read (SA tag)
    3. Drag the bar at the bottom edge of the track to resize it (210px here).
  4. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a BigWig file (.bw).This figure uses “pggb graph: pangenome depth (paths over K12)”.
    1. Drag the bar at the bottom edge of the track to resize it (100px here).
  5. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed MAF (.maf.gz + .tbi).This figure uses “pggb graph: whole-genome alignment (MAF, vs K12)”.
  6. Type your region of interest into the location box and press Enter.This figure is at chr:2,554,000-2,570,000.

Open this view in JBrowse Web ↗

Its genome and tracks are hosted, so File → Open track... there adds your own files beside them.

With your own data, the steps behind the figure:

  1. Put your genome in your JBrowse Web's config.json: jbrowse add-assembly adds it.This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “K12 genes”.
  3. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a BAM file (.bam + .bai).This figure uses “E146 nanopore reads (vs K12)”.
    1. Track menu → Read connections → View as pairs / link supplementary alignments (checked)
    2. Track menu → Group by... → Split read (SA tag)
    3. Drag the bar at the bottom edge of the track to resize it (210px here).
  4. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a BigWig file (.bw).This figure uses “pggb graph: pangenome depth (paths over K12)”.
    1. Drag the bar at the bottom edge of the track to resize it (100px here).
  5. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed MAF (.maf.gz + .tbi).This figure uses “pggb graph: whole-genome alignment (MAF, vs K12)”.
  6. Type your region of interest into the location box and press Enter.This figure is at chr:2,554,000-2,570,000.

This session spec draws the figure from https://jbrowse.org/demos/ecoli_pangenome/config.json: paste it after &session=spec- on a JBrowse Web link that loads that config.

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:2,554,000-2,570,000",
      "tracks": [
        {
          "trackId": "K12_genes",
          "type": "LinearBasicDisplay"
        },
        {
          "trackId": "ecoli_e146_ont",
          "type": "LinearAlignmentsDisplay",
          "linkedReads": "normal",
          "facet": "splitRead",
          "height": 210
        },
        {
          "trackId": "ecoli_pggb_depth",
          "type": "LinearWiggleDisplay",
          "height": 100
        },
        {
          "trackId": "ecoli_pggb_maf",
          "type": "LinearMafDisplay"
        }
      ]
    }
  ]
}

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/demos/ecoli_pangenome/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "K12",
            "loc": "chr:2,554,000-2,570,000",
            "tracks": [
                {
                    "trackId": "K12_genes",
                    "type": "LinearBasicDisplay"
                },
                {
                    "trackId": "ecoli_e146_ont",
                    "type": "LinearAlignmentsDisplay",
                    "linkedReads": "normal",
                    "facet": "splitRead",
                    "height": 210
                },
                {
                    "trackId": "ecoli_pggb_depth",
                    "type": "LinearWiggleDisplay",
                    "height": 100
                },
                {
                    "trackId": "ecoli_pggb_maf",
                    "type": "LinearMafDisplay"
                }
            ]
        }
    ],
)
app  # display the widget

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file with --bam, --vcfgz and the other file flags.

npx @jbrowse/img --config https://jbrowse.org/demos/ecoli_pangenome/config.json \
  --assembly K12 --loc chr:2,554,000-2,570,000 \
  --track K12_genes display:LinearBasicDisplay \
  --track ecoli_e146_ont display:LinearAlignmentsDisplay '{"linkedReads":"normal","facet":"splitRead","height":210}' \
  --track ecoli_pggb_depth display:LinearWiggleDisplay '{"height":100}' \
  --track ecoli_pggb_maf display:LinearMafDisplay \
  --width 1000 --out figure.svg

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:2,554,000-2,570,000",
      "tracks": [
        {
          "trackId": "K12_genes",
          "type": "LinearBasicDisplay"
        },
        {
          "trackId": "ecoli_e146_ont",
          "type": "LinearAlignmentsDisplay",
          "linkedReads": "normal",
          "facet": "splitRead",
          "height": 210
        },
        {
          "trackId": "ecoli_pggb_depth",
          "type": "LinearWiggleDisplay",
          "height": 100
        },
        {
          "trackId": "ecoli_pggb_maf",
          "type": "LinearMafDisplay"
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/ecoli_pangenome/config.json \
  --width 1000 --height 865 \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

💡 See also

The Minigraph-Cactus tutorial draws this window from its own graph's MAF, breaking at the same prophage edges, and plots both graphs' curves over one of those operons.

Per-strain presence

odgi pav splits depth per strain: it reports the fraction of each window that strain's path traverses. Load the set as one MultiQuantitativeTrack:

in_pggb odgi pav -i "/data/$og" -b /data/depth_windows.bed > pav.tsv
# K12 omitted: it is present over every window by construction
for strain in Sakai CFT073 NCTC86 IAI39; do
  # column 5 is the PanSN path, column 6 the presence fraction
  awk -F'\t' -v OFS='\t' -v g="${strain}#1#chr" \
    '$5 == g && $6 + 0 == $6 { print "chr", $2, $3, $6 }' pav.tsv |
    sort -k1,1 -k2,2n > "pav_${strain}.bedgraph"
  bedGraphToBigWig "pav_${strain}.bedgraph" chrom.sizes "ecoli_pggb_pav_${strain}.bw"
done

Goes in the tracks array of config.json. See Tracks.

{
  "type": "MultiQuantitativeTrack",
  "trackId": "ecoli_pggb_pav",
  "name": "pggb graph: per-strain presence (odgi pav, vs K12)",
  "assemblyNames": ["K12"],
  "adapter": {
    "type": "MultiWiggleAdapter",
    "subadapters": [
      {
        "type": "BigWigAdapter",
        "name": "Sakai",
        "uri": "ecoli_pggb_pav_Sakai.bw"
      },
      {
        "type": "BigWigAdapter",
        "name": "CFT073",
        "uri": "ecoli_pggb_pav_CFT073.bw"
      },
      {
        "type": "BigWigAdapter",
        "name": "NCTC86",
        "uri": "ecoli_pggb_pav_NCTC86.bw"
      },
      {
        "type": "BigWigAdapter",
        "name": "IAI39",
        "uri": "ecoli_pggb_pav_IAI39.bw"
      }
    ]
  }
}
jbrowse add-track-json '{
  "type": "MultiQuantitativeTrack",
  "trackId": "ecoli_pggb_pav",
  "name": "pggb graph: per-strain presence (odgi pav, vs K12)",
  "assemblyNames": ["K12"],
  "adapter": {
    "type": "MultiWiggleAdapter",
    "subadapters": [
      {
        "type": "BigWigAdapter",
        "name": "Sakai",
        "uri": "ecoli_pggb_pav_Sakai.bw"
      },
      {
        "type": "BigWigAdapter",
        "name": "CFT073",
        "uri": "ecoli_pggb_pav_CFT073.bw"
      },
      {
        "type": "BigWigAdapter",
        "name": "NCTC86",
        "uri": "ecoli_pggb_pav_NCTC86.bw"
      },
      {
        "type": "BigWigAdapter",
        "name": "IAI39",
        "uri": "ecoli_pggb_pav_IAI39.bw"
      }
    ]
  }
}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "MultiQuantitativeTrack",
  "trackId": "ecoli_pggb_pav",
  "name": "pggb graph: per-strain presence (odgi pav, vs K12)",
  "assemblyNames": ["K12"],
  "adapter": {
    "type": "MultiWiggleAdapter",
    "subadapters": [
      {
        "type": "BigWigAdapter",
        "name": "Sakai",
        "uri": "ecoli_pggb_pav_Sakai.bw"
      },
      {
        "type": "BigWigAdapter",
        "name": "CFT073",
        "uri": "ecoli_pggb_pav_CFT073.bw"
      },
      {
        "type": "BigWigAdapter",
        "name": "NCTC86",
        "uri": "ecoli_pggb_pav_NCTC86.bw"
      },
      {
        "type": "BigWigAdapter",
        "name": "IAI39",
        "uri": "ecoli_pggb_pav_IAI39.bw"
      }
    ]
  }
}

ecoli_pggb_pav_Sakai.bw, ecoli_pggb_pav_CFT073.bw, ecoli_pggb_pav_NCTC86.bw, ecoli_pggb_pav_IAI39.bw are relative to a config.json. Replace each with its URL or its path on this computer.

Under the curve, these rows show which strain each dip is missing: one row goes white over ybaL, and a second over the rhsD Rhs element.

The aggregate depth curve over all of K12, with odgi pav on the same windows below it, one row per non-K12 strain. Under the shaded span a single row goes white; the deepest troughs in the curve above are where all four do. Open this view in JBrowse ↗

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session.

Nothing happens?

Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22K12%22%2C%22loc%22%3A%22chr%3A1-4%2C641%2C652%22%2C%22highlight%22%3A%5B%7B%22refName%22%3A%22chr%22%2C%22start%22%3A501500%2C%22end%22%3A539000%2C%22color%22%3A%22rgba%28255%2C193%2C7%2C0.30%29%22%7D%5D%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22ecoli_pggb_depth%22%2C%22type%22%3A%22LinearWiggleDisplay%22%2C%22height%22%3A150%7D%2C%7B%22trackId%22%3A%22ecoli_pggb_pav%22%2C%22type%22%3A%22LinearWiggleDisplay%22%2C%22mark%22%3A%22heatmap%22%2C%22height%22%3A240%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+pangenome%2Fpav

With your own data, the steps behind the figure:

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a BigWig file (.bw).This figure uses “pggb graph: pangenome depth (paths over K12)”.
    1. Drag the bar at the bottom edge of the track to resize it (150px here).
  3. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “pggb graph: per-strain presence (odgi pav, vs K12)”.
    1. Track menu → Plot type → Density
    2. Drag the bar at the bottom edge of the track to resize it (240px here).
  4. Type your region of interest into the location box and press Enter.This figure is at chr:1-4,641,652.
  5. View menu → Zoom to region / use the location box, then add a highlightThis figure highlights 1 region; highlights can also be set with the &highlight= URL parameter.

Open this view in JBrowse Web ↗

Its genome and tracks are hosted, so File → Open track... there adds your own files beside them.

With your own data, the steps behind the figure:

  1. Put your genome in your JBrowse Web's config.json: jbrowse add-assembly adds it.This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a BigWig file (.bw).This figure uses “pggb graph: pangenome depth (paths over K12)”.
    1. Drag the bar at the bottom edge of the track to resize it (150px here).
  3. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “pggb graph: per-strain presence (odgi pav, vs K12)”.
    1. Track menu → Plot type → Density
    2. Drag the bar at the bottom edge of the track to resize it (240px here).
  4. Type your region of interest into the location box and press Enter.This figure is at chr:1-4,641,652.
  5. View menu → Zoom to region / use the location box, then add a highlightThis figure highlights 1 region; highlights can also be set with the &highlight= URL parameter.

This session spec draws the figure from https://jbrowse.org/demos/ecoli_pangenome/config.json: paste it after &session=spec- on a JBrowse Web link that loads that config.

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:1-4,641,652",
      "highlight": [
        {
          "refName": "chr",
          "start": 501500,
          "end": 539000,
          "color": "rgba(255,193,7,0.30)"
        }
      ],
      "tracks": [
        {
          "trackId": "ecoli_pggb_depth",
          "type": "LinearWiggleDisplay",
          "height": 150
        },
        {
          "trackId": "ecoli_pggb_pav",
          "type": "LinearWiggleDisplay",
          "mark": "heatmap",
          "height": 240
        }
      ]
    }
  ]
}

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/demos/ecoli_pangenome/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "K12",
            "loc": "chr:1-4,641,652",
            "highlight": [
                {
                    "refName": "chr",
                    "start": 501500,
                    "end": 539000,
                    "color": "rgba(255,193,7,0.30)"
                }
            ],
            "tracks": [
                {
                    "trackId": "ecoli_pggb_depth",
                    "type": "LinearWiggleDisplay",
                    "height": 150
                },
                {
                    "trackId": "ecoli_pggb_pav",
                    "type": "LinearWiggleDisplay",
                    "mark": "heatmap",
                    "height": 240
                }
            ]
        }
    ],
)
app  # display the widget

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file with --bam, --vcfgz and the other file flags.

npx @jbrowse/img --config https://jbrowse.org/demos/ecoli_pangenome/config.json \
  --assembly K12 --loc chr:1-4,641,652 \
  --track ecoli_pggb_depth display:LinearWiggleDisplay '{"height":150}' \
  --track ecoli_pggb_pav display:LinearWiggleDisplay '{"mark":"heatmap","height":240}' \
  --width 1000 --out figure.svg

It has no flag for this figure's highlight, so its picture can differ there.

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:1-4,641,652",
      "highlight": [
        {
          "refName": "chr",
          "start": 501500,
          "end": 539000,
          "color": "rgba(255,193,7,0.30)"
        }
      ],
      "tracks": [
        {
          "trackId": "ecoli_pggb_depth",
          "type": "LinearWiggleDisplay",
          "height": 150
        },
        {
          "trackId": "ecoli_pggb_pav",
          "type": "LinearWiggleDisplay",
          "mark": "heatmap",
          "height": 240
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/ecoli_pangenome/config.json \
  --width 1000 --height 640 \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

Compared to odgi viz

pggb rendered the graph in 1D with odgi viz (*.viz_*.png) and in 2D with odgi layout (*.lay.draw.png). The figure below is odgi viz re-run.

The five-strain graph drawn by odgi viz, one row per strain. The axis is graph node order, so its positions do not correspond to genes or to K12 coordinates.

The JBrowse projections below keep one row per strain, redrawn on K12's coordinates; the Minigraph-Cactus page marks the same 100 kb on both axes.

Drawing the graph as a graph

JBrowse can also draw the graph as a graph, through the graph genome view plugin; Pangenome (hosting your own graph) covers installing it and the one command that indexes a graph.

Browsing the whole graph by locus

Walking a P line in step order gives every segment an interval on that path, coordinates a plain GFA does not carry. build_pangenome_graph.sh does that walk and takes the graph's bubbles from the raw snarl VCF kept above:

curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/build_pangenome_graph.sh
bash build_pangenome_graph.sh "$gfa" ecoli_pggb --reference K12 --snarls ecoli_pggb_snarls.vcf.gz

The script writes the tabix-indexed segments, links, a coarse tier, and an ecoli_pggb.config.json. The uris below are our hosted copy; a local build uses ecoli_pggb instead:

Goes in the tracks array of config.json. See Tracks.

{
  "type": "FeatureTrack",
  "trackId": "ecoli_pggb_segments",
  "name": "pggb graph segments (whole graph, by locus)",
  "assemblyNames": ["K12"],
  "adapter": {
    "type": "RgfaTabixAdapter",
    "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb",
    "coarse": {
      "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50",
      "aboveBpPerPx": 1
    }
  },
  "displayDefaults": { "showLabels": "none" },
  "displays": [
    {
      "type": "LinearGraphDisplay",
      "displayId": "ecoli_pggb_segments-LinearGraphDisplay"
    },
    {
      "type": "LinearBasicDisplay",
      "displayId": "ecoli_pggb_segments-LinearBasicDisplay"
    }
  ]
}
jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "ecoli_pggb_segments",
  "name": "pggb graph segments (whole graph, by locus)",
  "assemblyNames": ["K12"],
  "adapter": {
    "type": "RgfaTabixAdapter",
    "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb",
    "coarse": {
      "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50",
      "aboveBpPerPx": 1
    }
  },
  "displayDefaults": { "showLabels": "none" },
  "displays": [
    {
      "type": "LinearGraphDisplay",
      "displayId": "ecoli_pggb_segments-LinearGraphDisplay"
    },
    {
      "type": "LinearBasicDisplay",
      "displayId": "ecoli_pggb_segments-LinearBasicDisplay"
    }
  ]
}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "FeatureTrack",
  "trackId": "ecoli_pggb_segments",
  "name": "pggb graph segments (whole graph, by locus)",
  "assemblyNames": ["K12"],
  "adapter": {
    "type": "RgfaTabixAdapter",
    "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb",
    "coarse": {
      "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50",
      "aboveBpPerPx": 1
    }
  },
  "displayDefaults": { "showLabels": "none" },
  "displays": [
    {
      "type": "LinearGraphDisplay",
      "displayId": "ecoli_pggb_segments-LinearGraphDisplay"
    },
    {
      "type": "LinearBasicDisplay",
      "displayId": "ecoli_pggb_segments-LinearBasicDisplay"
    }
  ]
}

A segment's name is its GFA id, cut every ~17 bp, so showLabels is off here and below.

Turned on, the track draws the window as a graph on K12's coordinates; Display types → Feature display draws it as a lane. A ruler drag offers Launch → Linear synteny view; the same menu on a synteny row's scale bar lets Replace current view re-anchor the stack.

One selection, a synteny stack: the Launch menu over a K12 window, the stack anchored on K12, and a drag on the Sakai row re-anchoring the stack on Sakai in place. Open the session this video starts in ↗

Open the session the video starts in ↗, then take the steps it shows:

  1. K-12: one lane per strain, and the graph segments
  2. Drag across the scale bar
  3. Stack the strains on the selection
  4. One panel per strain that aligns
  5. The stack, anchored on K-12, with its lanes on the top row
  6. Redraw the segments lane as the graph
  7. The graph, drawn inside the stack
  8. Drag on the Sakai row
  9. The same launch, from Sakai
  10. The same dialog, anchored on Sakai
  11. The stack re-anchored on Sakai

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session.

Nothing happens?

Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22K12%22%2C%22loc%22%3A%22chr%3A795%2C000-815%2C000%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22ecoli_ava%22%2C%22type%22%3A%22LGVSyntenyDisplay%22%2C%22facet%22%3A%22mateAssembly%22%2C%22hideSelfAlignments%22%3Atrue%2C%22featureHeight%22%3A14%2C%22height%22%3A135%7D%2C%7B%22trackId%22%3A%22ecoli_minigraph_segments%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22showLabels%22%3A%22none%22%2C%22height%22%3A60%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+synteny%2Fecoli_roundtrip

With your own data, the steps behind the figure:

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “E. coli pangenome (all-vs-all PAF)”.
    1. Track menu → Group by... → Mate assemblySynteny tracks only: one section per assembly on the other side of the alignment.
    2. Track menu → Group by... → Hide self-alignment lane (checked)Below a divider at the foot of that submenu, and only meaningful on an all-vs-all track, which is what has a self lane.
    3. Track menu → Feature height → Custom... → 14px
    4. Drag the bar at the bottom edge of the track to resize it (135px here).
  3. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “minigraph graph: rGFA segments (browsable by locus)”.
    1. Track menu → Show... → Labels → None
    2. Drag the bar at the bottom edge of the track to resize it (60px here).
  4. Type your region of interest into the location box and press Enter.This figure is at chr:795,000-815,000.

Open this view in JBrowse Web ↗

Its genome and tracks are hosted, so File → Open track... there adds your own files beside them.

With your own data, the steps behind the figure:

  1. Put your genome in your JBrowse Web's config.json: jbrowse add-assembly adds it.This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “E. coli pangenome (all-vs-all PAF)”.
    1. Track menu → Group by... → Mate assemblySynteny tracks only: one section per assembly on the other side of the alignment.
    2. Track menu → Group by... → Hide self-alignment lane (checked)Below a divider at the foot of that submenu, and only meaningful on an all-vs-all track, which is what has a self lane.
    3. Track menu → Feature height → Custom... → 14px
    4. Drag the bar at the bottom edge of the track to resize it (135px here).
  3. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “minigraph graph: rGFA segments (browsable by locus)”.
    1. Track menu → Show... → Labels → None
    2. Drag the bar at the bottom edge of the track to resize it (60px here).
  4. Type your region of interest into the location box and press Enter.This figure is at chr:795,000-815,000.

This session spec draws the figure from https://jbrowse.org/demos/ecoli_pangenome/config.json: paste it after &session=spec- on a JBrowse Web link that loads that config.

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:795,000-815,000",
      "tracks": [
        {
          "trackId": "ecoli_ava",
          "type": "LGVSyntenyDisplay",
          "facet": "mateAssembly",
          "hideSelfAlignments": true,
          "featureHeight": 14,
          "height": 135
        },
        {
          "trackId": "ecoli_minigraph_segments",
          "type": "LinearBasicDisplay",
          "showLabels": "none",
          "height": 60
        }
      ]
    }
  ]
}

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:795,000-815,000",
      "tracks": [
        {
          "trackId": "ecoli_ava",
          "type": "LGVSyntenyDisplay",
          "facet": "mateAssembly",
          "hideSelfAlignments": true,
          "featureHeight": 14,
          "height": 135
        },
        {
          "trackId": "ecoli_minigraph_segments",
          "type": "LinearBasicDisplay",
          "showLabels": "none",
          "height": 60
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/ecoli_pangenome/config.json \
  --width 1920 --height 1410 \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

Adding the track itself, from an empty session, is Open track... → Add pangenome graph track:

A K12 session with no graph in it, to a graph track: the track added through Open track... → Add pangenome graph track, the window narrowed onto the IS5 element, and the track drawing the graph on K12's coordinates. Open the session this video starts in ↗

Open the session the video starts in ↗, then take the steps it shows:

  1. Add the graph track from Open track...
  2. The track opens as the graph of the window
  3. chr:1,299,300-1,300,900
  4. Narrowed to the IS5 element, it cuts again

The track the video adds through the form, as the page above prints it:

{
  "type": "FeatureTrack",
  "trackId": "ecoli_pggb_segments",
  "name": "pggb graph segments (whole graph, by locus)",
  "assemblyNames": ["K12"],
  "adapter": {
    "type": "RgfaTabixAdapter",
    "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb",
    "coarse": {
      "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50",
      "aboveBpPerPx": 1
    }
  },
  "displayDefaults": { "showLabels": "none" },
  "displays": [
    {
      "type": "LinearGraphDisplay",
      "displayId": "ecoli_pggb_segments-LinearGraphDisplay"
    },
    {
      "type": "LinearBasicDisplay",
      "displayId": "ecoli_pggb_segments-LinearBasicDisplay"
    }
  ]
}

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session.

Nothing happens?

Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=test_data%2Fgraphgenomeview%2Fconfig.json&session=spec-%7B%22sessionTracks%22%3A%5B%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22K12_genes%22%2C%22name%22%3A%22K12+genes%22%2C%22assemblyNames%22%3A%5B%22K12%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22Gff3TabixAdapter%22%2C%22gffGzLocation%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2FK12.gff.gz%22%7D%2C%22index%22%3A%7B%22location%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2FK12.gff.gz.tbi%22%7D%7D%7D%7D%5D%2C%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22K12%22%2C%22loc%22%3A%22chr%3A1%2C290%2C000-1%2C310%2C000%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22K12_genes%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22height%22%3A70%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+pangenome%2Fpggb_subgraph_launch

With your own data, the steps behind the figure:

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “K12 genes”.
    1. Drag the bar at the bottom edge of the track to resize it (70px here).
  3. Type your region of interest into the location box and press Enter.This figure is at chr:1,290,000-1,310,000.

Open this view in JBrowse Web ↗

Its genome and tracks are hosted, so File → Open track... there adds your own files beside them.

With your own data, the steps behind the figure:

  1. Put your genome in your JBrowse Web's config.json: jbrowse add-assembly adds it.This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “K12 genes”.
    1. Drag the bar at the bottom edge of the track to resize it (70px here).
  3. Type your region of interest into the location box and press Enter.This figure is at chr:1,290,000-1,310,000.

A figure adds its tracks to one session. The jbrowse CLI writes the same tracks into a config.json instead, where every session that opens it has them: add-track where flags cover the whole track, add-track-json where they do not.

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "K12_genes",
  "name": "K12 genes",
  "assemblyNames": [
    "K12"
  ],
  "adapter": {
    "type": "Gff3TabixAdapter",
    "gffGzLocation": {
      "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
    },
    "index": {
      "location": {
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
      }
    }
  }
}'

Run these where the config.json is, or add --out <dir>, and point each uri at your own file. The config needs K12 already — jbrowse add-assembly adds yours. The location and the settings the steps carry are session state rather than track config — that half is the Spec tab, or jbrowse set-default-session.

This session spec draws the figure from test_data/graphgenomeview/config.json: paste it after &session=spec- on a JBrowse Web link that loads that config.

{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "K12_genes",
      "name": "K12 genes",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
          }
        }
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:1,290,000-1,310,000",
      "tracks": [
        {
          "trackId": "K12_genes",
          "type": "LinearBasicDisplay",
          "height": 70
        }
      ]
    }
  ]
}

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/code/jb2/main/test_data/graphgenomeview/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []) + [
        {
            "type": "FeatureTrack",
            "trackId": "K12_genes",
            "name": "K12 genes",
            "assemblyNames": [
                "K12"
            ],
            "adapter": {
                "type": "Gff3TabixAdapter",
                "gffGzLocation": {
                    "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
                },
                "index": {
                    "location": {
                        "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
                    }
                }
            }
        }
    ],
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "K12",
            "loc": "chr:1,290,000-1,310,000",
            "tracks": [
                {
                    "trackId": "K12_genes",
                    "type": "LinearBasicDisplay",
                    "height": 70
                }
            ]
        }
    ],
)
app  # display the widget

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file with --bam, --vcfgz and the other file flags.

cat > tracks.json <<'JSON'
[
  {
    "type": "FeatureTrack",
    "trackId": "K12_genes",
    "name": "K12 genes",
    "assemblyNames": [
      "K12"
    ],
    "adapter": {
      "type": "Gff3TabixAdapter",
      "gffGzLocation": {
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
      },
      "index": {
        "location": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
        }
      }
    }
  }
]
JSON

npx @jbrowse/img --config https://jbrowse.org/code/jb2/main/test_data/graphgenomeview/config.json \
  --tracks tracks.json \
  --assembly K12 --loc chr:1,290,000-1,310,000 \
  --track K12_genes display:LinearBasicDisplay '{"height":70}' \
  --width 1920 --out figure.svg

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "K12_genes",
      "name": "K12 genes",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
          }
        }
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:1,290,000-1,310,000",
      "tracks": [
        {
          "trackId": "K12_genes",
          "type": "LinearBasicDisplay",
          "height": 70
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/graphgenomeview/config.json \
  --width 1920 --height 1110 \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

In the force layout, a node's length is proportional to its sequence, so one long arm can swallow the drawing. Bubble spread → Compress lengths pulls the longest and shortest nodes towards the mean.

One node per bubble, when the window is wider than the graph can draw

The segments draw one node per GFA segment, about 17 bp each; the coarse tier draws one node per bubble instead, with the invariant reference as backbone. Its 50 bp threshold absorbs single-base alternatives and keeps every indel. The reference-position ramp colors agreeing stretches and paints charcoal where the strains differ.

The graph track names the tier coarse, handed over via aboveBpPerPx. Type chr:1,250,000-1,350,000, past one bp per pixel; the tier also loads as a separate track, whose Display types → Feature display draws it as a lane at any width:

Goes in the tracks array of config.json. See Tracks.

{
  "type": "FeatureTrack",
  "trackId": "ecoli_pggb_tier50",
  "name": "pggb graph bubbles (coarse tier, one node per bubble)",
  "assemblyNames": ["K12"],
  "adapter": {
    "type": "RgfaTabixAdapter",
    "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50"
  },
  "displays": [
    {
      "type": "LinearGraphDisplay",
      "displayId": "ecoli_pggb_tier50-LinearGraphDisplay"
    },
    {
      "type": "LinearBasicDisplay",
      "displayId": "ecoli_pggb_tier50-LinearBasicDisplay"
    }
  ]
}
jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "ecoli_pggb_tier50",
  "name": "pggb graph bubbles (coarse tier, one node per bubble)",
  "assemblyNames": ["K12"],
  "adapter": {
    "type": "RgfaTabixAdapter",
    "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50"
  },
  "displays": [
    {
      "type": "LinearGraphDisplay",
      "displayId": "ecoli_pggb_tier50-LinearGraphDisplay"
    },
    {
      "type": "LinearBasicDisplay",
      "displayId": "ecoli_pggb_tier50-LinearBasicDisplay"
    }
  ]
}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "FeatureTrack",
  "trackId": "ecoli_pggb_tier50",
  "name": "pggb graph bubbles (coarse tier, one node per bubble)",
  "assemblyNames": ["K12"],
  "adapter": {
    "type": "RgfaTabixAdapter",
    "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50"
  },
  "displays": [
    {
      "type": "LinearGraphDisplay",
      "displayId": "ecoli_pggb_tier50-LinearGraphDisplay"
    },
    {
      "type": "LinearBasicDisplay",
      "displayId": "ecoli_pggb_tier50-LinearBasicDisplay"
    }
  ]
}
100 kb of K12 around an IS5 element, one node per bubble: the tier as a lane above, and below it the graph track, which cuts from its tier at this zoom. The highlight and the boxed node are insH21, the IS5 element K12's annotation names, which K12 carries and the other four skip. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session.

Nothing happens?

Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=test_data%2Fgraphgenomeview%2Fconfig.json&session=spec-%7B%22sessionTracks%22%3A%5B%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22K12_genes%22%2C%22name%22%3A%22K12+genes%22%2C%22assemblyNames%22%3A%5B%22K12%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22Gff3TabixAdapter%22%2C%22gffGzLocation%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2FK12.gff.gz%22%7D%2C%22index%22%3A%7B%22location%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2FK12.gff.gz.tbi%22%7D%7D%7D%7D%2C%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22K12_insertion_sequences%22%2C%22name%22%3A%22K12+insertion+sequences%22%2C%22assemblyNames%22%3A%5B%22K12%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22Gff3TabixAdapter%22%2C%22gffGzLocation%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2FK12.gff.gz%22%7D%2C%22index%22%3A%7B%22location%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2FK12.gff.gz.tbi%22%7D%7D%7D%7D%2C%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22ecoli_pggb_tier50%22%2C%22name%22%3A%22pggb+graph+bubbles+%28coarse+tier%2C+one+node+per+bubble%29%22%2C%22assemblyNames%22%3A%5B%22K12%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22RgfaTabixAdapter%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fecoli_pggb.tier50%22%7D%7D%2C%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22ecoli_pggb_segments%22%2C%22name%22%3A%22pggb+graph+segments+%28whole+graph%2C+by+locus%29%22%2C%22assemblyNames%22%3A%5B%22K12%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22RgfaTabixAdapter%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fecoli_pggb%22%2C%22coarse%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fecoli_pggb.tier50%22%2C%22aboveBpPerPx%22%3A1%7D%7D%7D%5D%2C%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22K12%22%2C%22loc%22%3A%22chr%3A1%2C250%2C000-1%2C350%2C000%22%2C%22highlight%22%3A%5B%7B%22assemblyName%22%3A%22K12%22%2C%22refName%22%3A%22chr%22%2C%22start%22%3A1299497%2C%22end%22%3A1300697%2C%22color%22%3A%22rgba%2821%2C101%2C192%2C0.25%29%22%7D%5D%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22K12_insertion_sequences%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22jexlFilters%22%3A%5B%22startsWith%28get%28feature%2C%27name%27%29+%7C%7C+%27%27%2C%27ins%27%29%22%5D%2C%22height%22%3A50%7D%2C%7B%22trackId%22%3A%22ecoli_pggb_tier50%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22showLabels%22%3A%22none%22%2C%22height%22%3A50%2C%22color%22%3A%22jexl%3Aget%28feature%2C%27rank%27%29%3E0+%3F+%27rgb%2860%2C65%2C72%29%27+%3A+%27hsl%28%27+%2B+min%28300%2C+max%280%2C+%28%28get%28feature%2C%27start%27%29%2Bget%28feature%2C%27end%27%29%29%2F2+-+1250000%29+%2F+100000+*+300%29%29+%2B+%27%2C70%25%2C50%25%29%27%22%7D%2C%7B%22trackId%22%3A%22ecoli_pggb_segments%22%2C%22type%22%3A%22LinearGraphDisplay%22%2C%22colorScheme%22%3A%22reference-position%22%2C%22colorDomain%22%3A%7B%22start%22%3A1250000%2C%22end%22%3A1350000%7D%2C%22geneTrackId%22%3A%22K12_genes%22%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+pangenome%2Fpggb_bubble_tier

With your own data, the steps behind the figure:

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “K12 insertion sequences”.
    1. Track menu → Filter by... → add the expressionThis figure filters on startsWith(get(feature,'name') || '','ins').
    2. Drag the bar at the bottom edge of the track to resize it (50px here).
  3. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “pggb graph bubbles (coarse tier, one node per bubble)”.
    1. Track menu → Show... → Labels → None
    2. Drag the bar at the bottom edge of the track to resize it (50px here).
    3. Track menu → Settings → colorA per-feature expression. The Color by... radios write a solid color, a field's palette, and the strand colors only, so an expression is authored on the track config.
  4. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “pggb graph segments (whole graph, by locus)”.
    1. Track menu → Color → Reference position
  5. Type your region of interest into the location box and press Enter.This figure is at chr:1,250,000-1,350,000.
  6. View menu → Zoom to region / use the location box, then add a highlightThis figure highlights 1 region; highlights can also be set with the &highlight= URL parameter.

Some settings have no written step yet — see the Spec tab.

Open this view in JBrowse Web ↗

Its genome and tracks are hosted, so File → Open track... there adds your own files beside them.

With your own data, the steps behind the figure:

  1. Put your genome in your JBrowse Web's config.json: jbrowse add-assembly adds it.This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “K12 insertion sequences”.
    1. Track menu → Filter by... → add the expressionThis figure filters on startsWith(get(feature,'name') || '','ins').
    2. Drag the bar at the bottom edge of the track to resize it (50px here).
  3. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “pggb graph bubbles (coarse tier, one node per bubble)”.
    1. Track menu → Show... → Labels → None
    2. Drag the bar at the bottom edge of the track to resize it (50px here).
    3. Track menu → Settings → colorA per-feature expression. The Color by... radios write a solid color, a field's palette, and the strand colors only, so an expression is authored on the track config.
  4. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “pggb graph segments (whole graph, by locus)”.
    1. Track menu → Color → Reference position
  5. Type your region of interest into the location box and press Enter.This figure is at chr:1,250,000-1,350,000.
  6. View menu → Zoom to region / use the location box, then add a highlightThis figure highlights 1 region; highlights can also be set with the &highlight= URL parameter.

Some settings have no written step yet — see the Spec tab.

A figure adds its tracks to one session. The jbrowse CLI writes the same tracks into a config.json instead, where every session that opens it has them: add-track where flags cover the whole track, add-track-json where they do not.

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "K12_genes",
  "name": "K12 genes",
  "assemblyNames": [
    "K12"
  ],
  "adapter": {
    "type": "Gff3TabixAdapter",
    "gffGzLocation": {
      "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
    },
    "index": {
      "location": {
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
      }
    }
  }
}'

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "K12_insertion_sequences",
  "name": "K12 insertion sequences",
  "assemblyNames": [
    "K12"
  ],
  "adapter": {
    "type": "Gff3TabixAdapter",
    "gffGzLocation": {
      "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
    },
    "index": {
      "location": {
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
      }
    }
  }
}'

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "ecoli_pggb_tier50",
  "name": "pggb graph bubbles (coarse tier, one node per bubble)",
  "assemblyNames": [
    "K12"
  ],
  "adapter": {
    "type": "RgfaTabixAdapter",
    "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50"
  }
}'

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "ecoli_pggb_segments",
  "name": "pggb graph segments (whole graph, by locus)",
  "assemblyNames": [
    "K12"
  ],
  "adapter": {
    "type": "RgfaTabixAdapter",
    "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb",
    "coarse": {
      "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50",
      "aboveBpPerPx": 1
    }
  }
}'

Run these where the config.json is, or add --out <dir>, and point each uri at your own file. The config needs K12 already — jbrowse add-assembly adds yours. The location and the settings the steps carry are session state rather than track config — that half is the Spec tab, or jbrowse set-default-session.

This session spec draws the figure from test_data/graphgenomeview/config.json: paste it after &session=spec- on a JBrowse Web link that loads that config.

{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "K12_genes",
      "name": "K12 genes",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
          }
        }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "K12_insertion_sequences",
      "name": "K12 insertion sequences",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
          }
        }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_pggb_tier50",
      "name": "pggb graph bubbles (coarse tier, one node per bubble)",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50"
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_pggb_segments",
      "name": "pggb graph segments (whole graph, by locus)",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb",
        "coarse": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50",
          "aboveBpPerPx": 1
        }
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:1,250,000-1,350,000",
      "highlight": [
        {
          "assemblyName": "K12",
          "refName": "chr",
          "start": 1299497,
          "end": 1300697,
          "color": "rgba(21,101,192,0.25)"
        }
      ],
      "tracks": [
        {
          "trackId": "K12_insertion_sequences",
          "type": "LinearBasicDisplay",
          "jexlFilters": [
            "startsWith(get(feature,'name') || '','ins')"
          ],
          "height": 50
        },
        {
          "trackId": "ecoli_pggb_tier50",
          "type": "LinearBasicDisplay",
          "showLabels": "none",
          "height": 50,
          "color": "jexl:get(feature,'rank')>0 ? 'rgb(60,65,72)' : 'hsl(' + min(300, max(0, ((get(feature,'start')+get(feature,'end'))/2 - 1250000) / 100000 * 300)) + ',70%,50%)'"
        },
        {
          "trackId": "ecoli_pggb_segments",
          "type": "LinearGraphDisplay",
          "colorScheme": "reference-position",
          "colorDomain": {
            "start": 1250000,
            "end": 1350000
          },
          "geneTrackId": "K12_genes"
        }
      ]
    }
  ]
}

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "K12_genes",
      "name": "K12 genes",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
          }
        }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "K12_insertion_sequences",
      "name": "K12 insertion sequences",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
          }
        }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_pggb_tier50",
      "name": "pggb graph bubbles (coarse tier, one node per bubble)",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50"
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_pggb_segments",
      "name": "pggb graph segments (whole graph, by locus)",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb",
        "coarse": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50",
          "aboveBpPerPx": 1
        }
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:1,250,000-1,350,000",
      "highlight": [
        {
          "assemblyName": "K12",
          "refName": "chr",
          "start": 1299497,
          "end": 1300697,
          "color": "rgba(21,101,192,0.25)"
        }
      ],
      "tracks": [
        {
          "trackId": "K12_insertion_sequences",
          "type": "LinearBasicDisplay",
          "jexlFilters": [
            "startsWith(get(feature,'name') || '','ins')"
          ],
          "height": 50
        },
        {
          "trackId": "ecoli_pggb_tier50",
          "type": "LinearBasicDisplay",
          "showLabels": "none",
          "height": 50,
          "color": "jexl:get(feature,'rank')>0 ? 'rgb(60,65,72)' : 'hsl(' + min(300, max(0, ((get(feature,'start')+get(feature,'end'))/2 - 1250000) / 100000 * 300)) + ',70%,50%)'"
        },
        {
          "trackId": "ecoli_pggb_segments",
          "type": "LinearGraphDisplay",
          "colorScheme": "reference-position",
          "colorDomain": {
            "start": 1250000,
            "end": 1350000
          },
          "geneTrackId": "K12_genes"
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/graphgenomeview/config.json \
  --width 1000 --height 700 \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

Hover a node for the segments it collapsed. A tier node's Open in K12 takes the view to the span it stands for, and the graph track cuts the segments there.

The coarse tier's IS5 bubble taken down to the segments: hovering the node marks the K12 span it stands for in the lanes above, and the node's Open in K12 entry moves the view to that span, where the graph track cuts the segments. Open the session this video starts in ↗

Open the session the video starts in ↗, then take the steps it shows:

  1. Hover a node for the segments it collapses
  2. Open the bubble's span in the linear view
  3. Zoomed past the handover, the graph re-cuts from the segments

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session.

Nothing happens?

Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=test_data%2Fgraphgenomeview%2Fconfig.json&session=spec-%7B%22sessionTracks%22%3A%5B%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22K12_genes%22%2C%22name%22%3A%22K12+genes%22%2C%22assemblyNames%22%3A%5B%22K12%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22Gff3TabixAdapter%22%2C%22gffGzLocation%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2FK12.gff.gz%22%7D%2C%22index%22%3A%7B%22location%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2FK12.gff.gz.tbi%22%7D%7D%7D%7D%2C%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22ecoli_pggb_tier50%22%2C%22name%22%3A%22pggb+graph+bubbles+%28coarse+tier%2C+one+node+per+bubble%29%22%2C%22assemblyNames%22%3A%5B%22K12%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22RgfaTabixAdapter%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fecoli_pggb.tier50%22%7D%7D%2C%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22ecoli_pggb_segments%22%2C%22name%22%3A%22pggb+graph+segments+%28whole+graph%2C+by+locus%29%22%2C%22assemblyNames%22%3A%5B%22K12%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22RgfaTabixAdapter%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fecoli_pggb%22%2C%22coarse%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fecoli_pggb.tier50%22%2C%22aboveBpPerPx%22%3A1%7D%7D%7D%5D%2C%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22K12%22%2C%22loc%22%3A%22chr%3A1%2C250%2C000-1%2C350%2C000%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22K12_genes%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22height%22%3A70%7D%2C%7B%22trackId%22%3A%22ecoli_pggb_tier50%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22showLabels%22%3A%22none%22%2C%22height%22%3A50%2C%22color%22%3A%22jexl%3Aget%28feature%2C%27rank%27%29%3E0+%3F+%27rgb%2860%2C65%2C72%29%27+%3A+%27hsl%28%27+%2B+min%28300%2C+max%280%2C+%28%28get%28feature%2C%27start%27%29%2Bget%28feature%2C%27end%27%29%29%2F2+-+1250000%29+%2F+100000+*+300%29%29+%2B+%27%2C70%25%2C50%25%29%27%22%7D%2C%7B%22trackId%22%3A%22ecoli_pggb_segments%22%2C%22type%22%3A%22LinearGraphDisplay%22%2C%22colorScheme%22%3A%22reference-position%22%2C%22colorDomain%22%3A%7B%22start%22%3A1250000%2C%22end%22%3A1350000%7D%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+pangenome%2Ftier_to_fine

With your own data, the steps behind the figure:

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “K12 genes”.
    1. Drag the bar at the bottom edge of the track to resize it (70px here).
  3. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “pggb graph bubbles (coarse tier, one node per bubble)”.
    1. Track menu → Show... → Labels → None
    2. Drag the bar at the bottom edge of the track to resize it (50px here).
    3. Track menu → Settings → colorA per-feature expression. The Color by... radios write a solid color, a field's palette, and the strand colors only, so an expression is authored on the track config.
  4. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “pggb graph segments (whole graph, by locus)”.
    1. Track menu → Color → Reference position
  5. Type your region of interest into the location box and press Enter.This figure is at chr:1,250,000-1,350,000.

Some settings have no written step yet — see the Spec tab.

Open this view in JBrowse Web ↗

Its genome and tracks are hosted, so File → Open track... there adds your own files beside them.

With your own data, the steps behind the figure:

  1. Put your genome in your JBrowse Web's config.json: jbrowse add-assembly adds it.This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “K12 genes”.
    1. Drag the bar at the bottom edge of the track to resize it (70px here).
  3. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “pggb graph bubbles (coarse tier, one node per bubble)”.
    1. Track menu → Show... → Labels → None
    2. Drag the bar at the bottom edge of the track to resize it (50px here).
    3. Track menu → Settings → colorA per-feature expression. The Color by... radios write a solid color, a field's palette, and the strand colors only, so an expression is authored on the track config.
  4. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “pggb graph segments (whole graph, by locus)”.
    1. Track menu → Color → Reference position
  5. Type your region of interest into the location box and press Enter.This figure is at chr:1,250,000-1,350,000.

Some settings have no written step yet — see the Spec tab.

A figure adds its tracks to one session. The jbrowse CLI writes the same tracks into a config.json instead, where every session that opens it has them: add-track where flags cover the whole track, add-track-json where they do not.

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "K12_genes",
  "name": "K12 genes",
  "assemblyNames": [
    "K12"
  ],
  "adapter": {
    "type": "Gff3TabixAdapter",
    "gffGzLocation": {
      "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
    },
    "index": {
      "location": {
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
      }
    }
  }
}'

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "ecoli_pggb_tier50",
  "name": "pggb graph bubbles (coarse tier, one node per bubble)",
  "assemblyNames": [
    "K12"
  ],
  "adapter": {
    "type": "RgfaTabixAdapter",
    "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50"
  }
}'

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "ecoli_pggb_segments",
  "name": "pggb graph segments (whole graph, by locus)",
  "assemblyNames": [
    "K12"
  ],
  "adapter": {
    "type": "RgfaTabixAdapter",
    "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb",
    "coarse": {
      "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50",
      "aboveBpPerPx": 1
    }
  }
}'

Run these where the config.json is, or add --out <dir>, and point each uri at your own file. The config needs K12 already — jbrowse add-assembly adds yours. The location and the settings the steps carry are session state rather than track config — that half is the Spec tab, or jbrowse set-default-session.

This session spec draws the figure from test_data/graphgenomeview/config.json: paste it after &session=spec- on a JBrowse Web link that loads that config.

{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "K12_genes",
      "name": "K12 genes",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
          }
        }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_pggb_tier50",
      "name": "pggb graph bubbles (coarse tier, one node per bubble)",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50"
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_pggb_segments",
      "name": "pggb graph segments (whole graph, by locus)",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb",
        "coarse": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50",
          "aboveBpPerPx": 1
        }
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:1,250,000-1,350,000",
      "tracks": [
        {
          "trackId": "K12_genes",
          "type": "LinearBasicDisplay",
          "height": 70
        },
        {
          "trackId": "ecoli_pggb_tier50",
          "type": "LinearBasicDisplay",
          "showLabels": "none",
          "height": 50,
          "color": "jexl:get(feature,'rank')>0 ? 'rgb(60,65,72)' : 'hsl(' + min(300, max(0, ((get(feature,'start')+get(feature,'end'))/2 - 1250000) / 100000 * 300)) + ',70%,50%)'"
        },
        {
          "trackId": "ecoli_pggb_segments",
          "type": "LinearGraphDisplay",
          "colorScheme": "reference-position",
          "colorDomain": {
            "start": 1250000,
            "end": 1350000
          }
        }
      ]
    }
  ]
}

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "K12_genes",
      "name": "K12 genes",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
          }
        }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_pggb_tier50",
      "name": "pggb graph bubbles (coarse tier, one node per bubble)",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50"
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_pggb_segments",
      "name": "pggb graph segments (whole graph, by locus)",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb",
        "coarse": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50",
          "aboveBpPerPx": 1
        }
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:1,250,000-1,350,000",
      "tracks": [
        {
          "trackId": "K12_genes",
          "type": "LinearBasicDisplay",
          "height": 70
        },
        {
          "trackId": "ecoli_pggb_tier50",
          "type": "LinearBasicDisplay",
          "showLabels": "none",
          "height": 50,
          "color": "jexl:get(feature,'rank')>0 ? 'rgb(60,65,72)' : 'hsl(' + min(300, max(0, ((get(feature,'start')+get(feature,'end'))/2 - 1250000) / 100000 * 300)) + ',70%,50%)'"
        },
        {
          "trackId": "ecoli_pggb_segments",
          "type": "LinearGraphDisplay",
          "colorScheme": "reference-position",
          "colorDomain": {
            "start": 1250000,
            "end": 1350000
          }
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/graphgenomeview/config.json \
  --width 1920 --height 810 \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

Layout → Sample rows gives each strain a separate row: carriage on this graph, build order (minigraph's SR) on an rGFA.

Sample rows reads each segment individually. Type chr:1,004,500-1,004,961; a row's bar is drawn over the reference it replaces, so CFT073's row draws one long bar labelled 7 kb del for a 75 bp segment.

In Sample rows the top row is K12's backbone; each strain's marks below are the segments it takes instead, in the MAF's row order.

460 bp at the ycbF/pyrD boundary in Sample rows, under the MAF lane. CFT073's row is the long bar running off the left edge, and its MAF row is empty over the same span. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session.

Nothing happens?

Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=test_data%2Fgraphgenomeview%2Fconfig.json&session=spec-%7B%22sessionTracks%22%3A%5B%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22K12_genes%22%2C%22name%22%3A%22K12+genes%22%2C%22assemblyNames%22%3A%5B%22K12%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22Gff3TabixAdapter%22%2C%22gffGzLocation%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2FK12.gff.gz%22%7D%2C%22index%22%3A%7B%22location%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2FK12.gff.gz.tbi%22%7D%7D%7D%7D%2C%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22ecoli_pggb_segments%22%2C%22name%22%3A%22pggb+graph+segments+%28whole+graph%2C+by+locus%29%22%2C%22assemblyNames%22%3A%5B%22K12%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22RgfaTabixAdapter%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fecoli_pggb%22%2C%22coarse%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fecoli_pggb.tier50%22%2C%22aboveBpPerPx%22%3A1%7D%7D%7D%2C%7B%22type%22%3A%22MafTrack%22%2C%22trackId%22%3A%22ecoli_pggb_maf%22%2C%22name%22%3A%22pggb+graph%3A+whole-genome+alignment+%28MAF%2C+vs+K12%29%22%2C%22assemblyNames%22%3A%5B%22K12%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22MafTabixAdapter%22%2C%22samples%22%3A%5B%22K12%22%2C%22Sakai%22%2C%22CFT073%22%2C%22NCTC86%22%2C%22IAI39%22%5D%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fecoli_pggb.maf.bed.gz%22%7D%7D%5D%2C%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22K12%22%2C%22loc%22%3A%22chr%3A1%2C004%2C500-1%2C004%2C961%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22K12_genes%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22height%22%3A70%7D%2C%7B%22trackId%22%3A%22ecoli_pggb_maf%22%2C%22type%22%3A%22LinearMafDisplay%22%2C%22rows%22%3A%7B%22domain%22%3A%5B%22K12%22%2C%22CFT073%22%2C%22IAI39%22%2C%22NCTC86%22%2C%22Sakai%22%5D%7D%2C%22showTree%22%3Atrue%2C%22height%22%3A150%7D%2C%7B%22trackId%22%3A%22ecoli_pggb_segments%22%2C%22type%22%3A%22LinearGraphDisplay%22%2C%22layoutMode%22%3A%22samplerows%22%2C%22colorScheme%22%3A%22reference-position%22%2C%22colorDomain%22%3A%7B%22start%22%3A1004500%2C%22end%22%3A1004961%7D%2C%22maxRegionBp%22%3A508%2C%22showBubbles%22%3Afalse%2C%22height%22%3A600%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+pangenome%2Fpggb_locus_sample_rows

With your own data, the steps behind the figure:

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “K12 genes”.
    1. Drag the bar at the bottom edge of the track to resize it (70px here).
  3. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed MAF (.maf.gz + .tbi).This figure uses “pggb graph: whole-genome alignment (MAF, vs K12)”.
    1. Track menu → Edit colors/arrangement... → drag the rows into orderThe same dialog renames a row and recolors it, so a figure's 5 rows carry their order, any labels it shows, and any color it picked.
    2. Track menu → Show... → Show tree (checked)On by default. The item is disabled until there is a tree to show — a clustering run, or a MAF track’s guide tree; the row labels have their own toggle beneath it.
    3. Drag the bar at the bottom edge of the track to resize it (150px here).
  4. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “pggb graph segments (whole graph, by locus)”.
    1. Track menu → Layout → Sample rows
    2. Track menu → Color → Reference position
    3. Track menu → Mark bubbles (unchecked)
    4. Drag the bar at the bottom edge of the track to resize it (600px here).
  5. Type your region of interest into the location box and press Enter.This figure is at chr:1,004,500-1,004,961.

Some settings have no written step yet — see the Spec tab.

Open this view in JBrowse Web ↗

Its genome and tracks are hosted, so File → Open track... there adds your own files beside them.

With your own data, the steps behind the figure:

  1. Put your genome in your JBrowse Web's config.json: jbrowse add-assembly adds it.This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “K12 genes”.
    1. Drag the bar at the bottom edge of the track to resize it (70px here).
  3. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed MAF (.maf.gz + .tbi).This figure uses “pggb graph: whole-genome alignment (MAF, vs K12)”.
    1. Track menu → Edit colors/arrangement... → drag the rows into orderThe same dialog renames a row and recolors it, so a figure's 5 rows carry their order, any labels it shows, and any color it picked.
    2. Track menu → Show... → Show tree (checked)On by default. The item is disabled until there is a tree to show — a clustering run, or a MAF track’s guide tree; the row labels have their own toggle beneath it.
    3. Drag the bar at the bottom edge of the track to resize it (150px here).
  4. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “pggb graph segments (whole graph, by locus)”.
    1. Track menu → Layout → Sample rows
    2. Track menu → Color → Reference position
    3. Track menu → Mark bubbles (unchecked)
    4. Drag the bar at the bottom edge of the track to resize it (600px here).
  5. Type your region of interest into the location box and press Enter.This figure is at chr:1,004,500-1,004,961.

Some settings have no written step yet — see the Spec tab.

A figure adds its tracks to one session. The jbrowse CLI writes the same tracks into a config.json instead, where every session that opens it has them: add-track where flags cover the whole track, add-track-json where they do not.

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "K12_genes",
  "name": "K12 genes",
  "assemblyNames": [
    "K12"
  ],
  "adapter": {
    "type": "Gff3TabixAdapter",
    "gffGzLocation": {
      "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
    },
    "index": {
      "location": {
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
      }
    }
  }
}'

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "ecoli_pggb_segments",
  "name": "pggb graph segments (whole graph, by locus)",
  "assemblyNames": [
    "K12"
  ],
  "adapter": {
    "type": "RgfaTabixAdapter",
    "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb",
    "coarse": {
      "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50",
      "aboveBpPerPx": 1
    }
  }
}'

jbrowse add-track-json '{
  "type": "MafTrack",
  "trackId": "ecoli_pggb_maf",
  "name": "pggb graph: whole-genome alignment (MAF, vs K12)",
  "assemblyNames": [
    "K12"
  ],
  "adapter": {
    "type": "MafTabixAdapter",
    "samples": [
      "K12",
      "Sakai",
      "CFT073",
      "NCTC86",
      "IAI39"
    ],
    "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.maf.bed.gz"
  }
}'

Run these where the config.json is, or add --out <dir>, and point each uri at your own file. The config needs K12 already — jbrowse add-assembly adds yours. The location and the settings the steps carry are session state rather than track config — that half is the Spec tab, or jbrowse set-default-session.

This session spec draws the figure from test_data/graphgenomeview/config.json: paste it after &session=spec- on a JBrowse Web link that loads that config.

{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "K12_genes",
      "name": "K12 genes",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
          }
        }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_pggb_segments",
      "name": "pggb graph segments (whole graph, by locus)",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb",
        "coarse": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50",
          "aboveBpPerPx": 1
        }
      }
    },
    {
      "type": "MafTrack",
      "trackId": "ecoli_pggb_maf",
      "name": "pggb graph: whole-genome alignment (MAF, vs K12)",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "MafTabixAdapter",
        "samples": [
          "K12",
          "Sakai",
          "CFT073",
          "NCTC86",
          "IAI39"
        ],
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.maf.bed.gz"
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:1,004,500-1,004,961",
      "tracks": [
        {
          "trackId": "K12_genes",
          "type": "LinearBasicDisplay",
          "height": 70
        },
        {
          "trackId": "ecoli_pggb_maf",
          "type": "LinearMafDisplay",
          "rows": {
            "domain": [
              "K12",
              "CFT073",
              "IAI39",
              "NCTC86",
              "Sakai"
            ]
          },
          "showTree": true,
          "height": 150
        },
        {
          "trackId": "ecoli_pggb_segments",
          "type": "LinearGraphDisplay",
          "layoutMode": "samplerows",
          "colorScheme": "reference-position",
          "colorDomain": {
            "start": 1004500,
            "end": 1004961
          },
          "maxRegionBp": 508,
          "showBubbles": false,
          "height": 600
        }
      ]
    }
  ]
}

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "K12_genes",
      "name": "K12 genes",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
          }
        }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_pggb_segments",
      "name": "pggb graph segments (whole graph, by locus)",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb",
        "coarse": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50",
          "aboveBpPerPx": 1
        }
      }
    },
    {
      "type": "MafTrack",
      "trackId": "ecoli_pggb_maf",
      "name": "pggb graph: whole-genome alignment (MAF, vs K12)",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "MafTabixAdapter",
        "samples": [
          "K12",
          "Sakai",
          "CFT073",
          "NCTC86",
          "IAI39"
        ],
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.maf.bed.gz"
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:1,004,500-1,004,961",
      "tracks": [
        {
          "trackId": "K12_genes",
          "type": "LinearBasicDisplay",
          "height": 70
        },
        {
          "trackId": "ecoli_pggb_maf",
          "type": "LinearMafDisplay",
          "rows": {
            "domain": [
              "K12",
              "CFT073",
              "IAI39",
              "NCTC86",
              "Sakai"
            ]
          },
          "showTree": true,
          "height": 150
        },
        {
          "trackId": "ecoli_pggb_segments",
          "type": "LinearGraphDisplay",
          "layoutMode": "samplerows",
          "colorScheme": "reference-position",
          "colorDomain": {
            "start": 1004500,
            "end": 1004961
          },
          "maxRegionBp": 508,
          "showBubbles": false,
          "height": 600
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/graphgenomeview/config.json \
  --width 1000 --height 1120 \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

Layout → Force-directed layout redraws the same nodes by their shape, with no reference axis, until Layout → Sample rows puts them back on K12's:

The same 460 bp through the track menu's Layout submenu. Sample rows holds the nodes to the reference axis, one row per strain; the force drawing drops the axis, and the alternate routes extend from the backbone where the rows had flattened them. Open the session this video starts in ↗

Open the session the video starts in ↗, then take the steps it shows:

  1. Re-lay the same rows out with the force engine

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session.

Nothing happens?

Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=test_data%2Fgraphgenomeview%2Fconfig.json&session=spec-%7B%22sessionTracks%22%3A%5B%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22K12_genes%22%2C%22name%22%3A%22K12+genes%22%2C%22assemblyNames%22%3A%5B%22K12%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22Gff3TabixAdapter%22%2C%22gffGzLocation%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2FK12.gff.gz%22%7D%2C%22index%22%3A%7B%22location%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2FK12.gff.gz.tbi%22%7D%7D%7D%7D%2C%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22ecoli_pggb_segments%22%2C%22name%22%3A%22pggb+graph+segments+%28whole+graph%2C+by+locus%29%22%2C%22assemblyNames%22%3A%5B%22K12%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22RgfaTabixAdapter%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fecoli_pggb%22%2C%22coarse%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fecoli_pggb.tier50%22%2C%22aboveBpPerPx%22%3A1%7D%7D%7D%2C%7B%22type%22%3A%22MafTrack%22%2C%22trackId%22%3A%22ecoli_pggb_maf%22%2C%22name%22%3A%22pggb+graph%3A+whole-genome+alignment+%28MAF%2C+vs+K12%29%22%2C%22assemblyNames%22%3A%5B%22K12%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22MafTabixAdapter%22%2C%22samples%22%3A%5B%22K12%22%2C%22Sakai%22%2C%22CFT073%22%2C%22NCTC86%22%2C%22IAI39%22%5D%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fecoli_pggb.maf.bed.gz%22%7D%7D%5D%2C%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22K12%22%2C%22loc%22%3A%22chr%3A1%2C004%2C500-1%2C004%2C961%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22K12_genes%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22height%22%3A70%7D%2C%7B%22trackId%22%3A%22ecoli_pggb_maf%22%2C%22type%22%3A%22LinearMafDisplay%22%2C%22rows%22%3A%7B%22domain%22%3A%5B%22K12%22%2C%22CFT073%22%2C%22IAI39%22%2C%22NCTC86%22%2C%22Sakai%22%5D%7D%2C%22showTree%22%3Atrue%2C%22height%22%3A150%7D%2C%7B%22trackId%22%3A%22ecoli_pggb_segments%22%2C%22type%22%3A%22LinearGraphDisplay%22%2C%22layoutMode%22%3A%22samplerows%22%2C%22colorScheme%22%3A%22reference-position%22%2C%22colorDomain%22%3A%7B%22start%22%3A1004500%2C%22end%22%3A1004961%7D%2C%22maxRegionBp%22%3A508%2C%22height%22%3A600%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+pangenome%2Fpggb_layout_switch

With your own data, the steps behind the figure:

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “K12 genes”.
    1. Drag the bar at the bottom edge of the track to resize it (70px here).
  3. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed MAF (.maf.gz + .tbi).This figure uses “pggb graph: whole-genome alignment (MAF, vs K12)”.
    1. Track menu → Edit colors/arrangement... → drag the rows into orderThe same dialog renames a row and recolors it, so a figure's 5 rows carry their order, any labels it shows, and any color it picked.
    2. Track menu → Show... → Show tree (checked)On by default. The item is disabled until there is a tree to show — a clustering run, or a MAF track’s guide tree; the row labels have their own toggle beneath it.
    3. Drag the bar at the bottom edge of the track to resize it (150px here).
  4. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “pggb graph segments (whole graph, by locus)”.
    1. Track menu → Layout → Sample rows
    2. Track menu → Color → Reference position
    3. Drag the bar at the bottom edge of the track to resize it (600px here).
  5. Type your region of interest into the location box and press Enter.This figure is at chr:1,004,500-1,004,961.

Some settings have no written step yet — see the Spec tab.

Open this view in JBrowse Web ↗

Its genome and tracks are hosted, so File → Open track... there adds your own files beside them.

With your own data, the steps behind the figure:

  1. Put your genome in your JBrowse Web's config.json: jbrowse add-assembly adds it.This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “K12 genes”.
    1. Drag the bar at the bottom edge of the track to resize it (70px here).
  3. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed MAF (.maf.gz + .tbi).This figure uses “pggb graph: whole-genome alignment (MAF, vs K12)”.
    1. Track menu → Edit colors/arrangement... → drag the rows into orderThe same dialog renames a row and recolors it, so a figure's 5 rows carry their order, any labels it shows, and any color it picked.
    2. Track menu → Show... → Show tree (checked)On by default. The item is disabled until there is a tree to show — a clustering run, or a MAF track’s guide tree; the row labels have their own toggle beneath it.
    3. Drag the bar at the bottom edge of the track to resize it (150px here).
  4. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “pggb graph segments (whole graph, by locus)”.
    1. Track menu → Layout → Sample rows
    2. Track menu → Color → Reference position
    3. Drag the bar at the bottom edge of the track to resize it (600px here).
  5. Type your region of interest into the location box and press Enter.This figure is at chr:1,004,500-1,004,961.

Some settings have no written step yet — see the Spec tab.

A figure adds its tracks to one session. The jbrowse CLI writes the same tracks into a config.json instead, where every session that opens it has them: add-track where flags cover the whole track, add-track-json where they do not.

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "K12_genes",
  "name": "K12 genes",
  "assemblyNames": [
    "K12"
  ],
  "adapter": {
    "type": "Gff3TabixAdapter",
    "gffGzLocation": {
      "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
    },
    "index": {
      "location": {
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
      }
    }
  }
}'

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "ecoli_pggb_segments",
  "name": "pggb graph segments (whole graph, by locus)",
  "assemblyNames": [
    "K12"
  ],
  "adapter": {
    "type": "RgfaTabixAdapter",
    "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb",
    "coarse": {
      "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50",
      "aboveBpPerPx": 1
    }
  }
}'

jbrowse add-track-json '{
  "type": "MafTrack",
  "trackId": "ecoli_pggb_maf",
  "name": "pggb graph: whole-genome alignment (MAF, vs K12)",
  "assemblyNames": [
    "K12"
  ],
  "adapter": {
    "type": "MafTabixAdapter",
    "samples": [
      "K12",
      "Sakai",
      "CFT073",
      "NCTC86",
      "IAI39"
    ],
    "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.maf.bed.gz"
  }
}'

Run these where the config.json is, or add --out <dir>, and point each uri at your own file. The config needs K12 already — jbrowse add-assembly adds yours. The location and the settings the steps carry are session state rather than track config — that half is the Spec tab, or jbrowse set-default-session.

This session spec draws the figure from test_data/graphgenomeview/config.json: paste it after &session=spec- on a JBrowse Web link that loads that config.

{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "K12_genes",
      "name": "K12 genes",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
          }
        }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_pggb_segments",
      "name": "pggb graph segments (whole graph, by locus)",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb",
        "coarse": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50",
          "aboveBpPerPx": 1
        }
      }
    },
    {
      "type": "MafTrack",
      "trackId": "ecoli_pggb_maf",
      "name": "pggb graph: whole-genome alignment (MAF, vs K12)",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "MafTabixAdapter",
        "samples": [
          "K12",
          "Sakai",
          "CFT073",
          "NCTC86",
          "IAI39"
        ],
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.maf.bed.gz"
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:1,004,500-1,004,961",
      "tracks": [
        {
          "trackId": "K12_genes",
          "type": "LinearBasicDisplay",
          "height": 70
        },
        {
          "trackId": "ecoli_pggb_maf",
          "type": "LinearMafDisplay",
          "rows": {
            "domain": [
              "K12",
              "CFT073",
              "IAI39",
              "NCTC86",
              "Sakai"
            ]
          },
          "showTree": true,
          "height": 150
        },
        {
          "trackId": "ecoli_pggb_segments",
          "type": "LinearGraphDisplay",
          "layoutMode": "samplerows",
          "colorScheme": "reference-position",
          "colorDomain": {
            "start": 1004500,
            "end": 1004961
          },
          "maxRegionBp": 508,
          "height": 600
        }
      ]
    }
  ]
}

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "K12_genes",
      "name": "K12 genes",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
          }
        }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_pggb_segments",
      "name": "pggb graph segments (whole graph, by locus)",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb",
        "coarse": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50",
          "aboveBpPerPx": 1
        }
      }
    },
    {
      "type": "MafTrack",
      "trackId": "ecoli_pggb_maf",
      "name": "pggb graph: whole-genome alignment (MAF, vs K12)",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "MafTabixAdapter",
        "samples": [
          "K12",
          "Sakai",
          "CFT073",
          "NCTC86",
          "IAI39"
        ],
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.maf.bed.gz"
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:1,004,500-1,004,961",
      "tracks": [
        {
          "trackId": "K12_genes",
          "type": "LinearBasicDisplay",
          "height": 70
        },
        {
          "trackId": "ecoli_pggb_maf",
          "type": "LinearMafDisplay",
          "rows": {
            "domain": [
              "K12",
              "CFT073",
              "IAI39",
              "NCTC86",
              "Sakai"
            ]
          },
          "showTree": true,
          "height": 150
        },
        {
          "trackId": "ecoli_pggb_segments",
          "type": "LinearGraphDisplay",
          "layoutMode": "samplerows",
          "colorScheme": "reference-position",
          "colorDomain": {
            "start": 1004500,
            "end": 1004961
          },
          "maxRegionBp": 508,
          "height": 600
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/graphgenomeview/config.json \
  --width 1920 --height 1250 \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

Who carries a segment

Clicking a node opens its details, including carriedBy: every haplotype walking that segment, recorded as an SM:Z: tag.

Carriage as a linear lane

The SM:Z: tag reaches the segments track as attributes: samples is the haplotype list and carriers its length, which the color paints by:

Goes in the tracks array of config.json. See Tracks.

{
  "type": "FeatureTrack",
  "trackId": "ecoli_pggb_carriage",
  "name": "pggb graph: segment carriage",
  "assemblyNames": ["K12"],
  "adapter": {
    "type": "RgfaTabixAdapter",
    "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb"
  },
  "displays": [
    {
      "type": "LinearBasicDisplay",
      "displayId": "ecoli_pggb_carriage-LinearBasicDisplay",
      "displayMode": "collapsed",
      "showLabels": false,
      "color": {
        "field": "carriers",
        "domain": ["5", "4", "3", "2", "1"],
        "range": ["#bdbdbd", "#fed976", "#feb24c", "#fd8d3c", "#e31a1c"],
        "labels": [
          "All 5 strains (core)",
          "4 strains",
          "3 strains",
          "2 strains",
          "1 strain (private)"
        ],
        "title": "Strains carrying"
      }
    }
  ]
}
jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "ecoli_pggb_carriage",
  "name": "pggb graph: segment carriage",
  "assemblyNames": ["K12"],
  "adapter": {
    "type": "RgfaTabixAdapter",
    "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb"
  },
  "displays": [
    {
      "type": "LinearBasicDisplay",
      "displayId": "ecoli_pggb_carriage-LinearBasicDisplay",
      "displayMode": "collapsed",
      "showLabels": false,
      "color": {
        "field": "carriers",
        "domain": ["5", "4", "3", "2", "1"],
        "range": ["#bdbdbd", "#fed976", "#feb24c", "#fd8d3c", "#e31a1c"],
        "labels": [
          "All 5 strains (core)",
          "4 strains",
          "3 strains",
          "2 strains",
          "1 strain (private)"
        ],
        "title": "Strains carrying"
      }
    }
  ]
}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "FeatureTrack",
  "trackId": "ecoli_pggb_carriage",
  "name": "pggb graph: segment carriage",
  "assemblyNames": ["K12"],
  "adapter": {
    "type": "RgfaTabixAdapter",
    "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb"
  },
  "displays": [
    {
      "type": "LinearBasicDisplay",
      "displayId": "ecoli_pggb_carriage-LinearBasicDisplay",
      "displayMode": "collapsed",
      "showLabels": false,
      "color": {
        "field": "carriers",
        "domain": ["5", "4", "3", "2", "1"],
        "range": ["#bdbdbd", "#fed976", "#feb24c", "#fd8d3c", "#e31a1c"],
        "labels": [
          "All 5 strains (core)",
          "4 strains",
          "3 strains",
          "2 strains",
          "1 strain (private)"
        ],
        "title": "Strains carrying"
      }
    }
  ]
}
Who carries the IS5 element at K12 chr:1,299,499-1,300,693. The carriage lane is a feature track colored by the GFA SM:Z: tag's strain count, so the red box is a segment K12 alone walks. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session.

Nothing happens?

Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=test_data%2Fgraphgenomeview%2Fconfig.json&session=spec-%7B%22sessionTracks%22%3A%5B%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22K12_genes%22%2C%22name%22%3A%22K12+genes%22%2C%22assemblyNames%22%3A%5B%22K12%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22Gff3TabixAdapter%22%2C%22gffGzLocation%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2FK12.gff.gz%22%7D%2C%22index%22%3A%7B%22location%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2FK12.gff.gz.tbi%22%7D%7D%7D%7D%2C%7B%22type%22%3A%22QuantitativeTrack%22%2C%22trackId%22%3A%22ecoli_pggb_depth%22%2C%22name%22%3A%22pggb+graph%3A+pangenome+depth+%28paths+over+K12%29%22%2C%22assemblyNames%22%3A%5B%22K12%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22BigWigAdapter%22%2C%22bigWigLocation%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fecoli_pggb_depth.bw%22%7D%7D%7D%2C%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22ecoli_pggb_carriage%22%2C%22name%22%3A%22pggb+graph%3A+segment+carriage%22%2C%22assemblyNames%22%3A%5B%22K12%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22RgfaTabixAdapter%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fecoli_pggb%22%7D%7D%5D%2C%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22K12%22%2C%22loc%22%3A%22chr%3A1%2C299%2C300-1%2C300%2C900%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22K12_genes%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22height%22%3A70%7D%2C%7B%22trackId%22%3A%22ecoli_pggb_depth%22%2C%22type%22%3A%22LinearWiggleDisplay%22%2C%22height%22%3A100%7D%2C%7B%22trackId%22%3A%22ecoli_pggb_carriage%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22displayMode%22%3A%22collapsed%22%2C%22showLabels%22%3A%22none%22%2C%22height%22%3A150%2C%22color%22%3A%7B%22field%22%3A%22carriers%22%2C%22domain%22%3A%5B%225%22%2C%224%22%2C%223%22%2C%222%22%2C%221%22%5D%2C%22range%22%3A%5B%22%23bdbdbd%22%2C%22%23fed976%22%2C%22%23feb24c%22%2C%22%23fd8d3c%22%2C%22%23e31a1c%22%5D%2C%22labels%22%3A%5B%22All+5+strains+%28core%29%22%2C%224+strains%22%2C%223+strains%22%2C%222+strains%22%2C%221+strain+%28private%29%22%5D%2C%22title%22%3A%22Strains+carrying%22%7D%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+pangenome%2Fpggb_carriage_lane

With your own data, the steps behind the figure:

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “K12 genes”.
    1. Drag the bar at the bottom edge of the track to resize it (70px here).
  3. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a BigWig file (.bw).This figure uses “pggb graph: pangenome depth (paths over K12)”.
    1. Drag the bar at the bottom edge of the track to resize it (100px here).
  4. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “pggb graph: segment carriage”.
    1. Track menu → Feature height → Collapsed
    2. Track menu → Show... → Labels → None
    3. Drag the bar at the bottom edge of the track to resize it (150px here).
    4. Track menu → Color by... → Attribute... → Edit as JSON...
  5. Type your region of interest into the location box and press Enter.This figure is at chr:1,299,300-1,300,900.

Open this view in JBrowse Web ↗

Its genome and tracks are hosted, so File → Open track... there adds your own files beside them.

With your own data, the steps behind the figure:

  1. Put your genome in your JBrowse Web's config.json: jbrowse add-assembly adds it.This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “K12 genes”.
    1. Drag the bar at the bottom edge of the track to resize it (70px here).
  3. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a BigWig file (.bw).This figure uses “pggb graph: pangenome depth (paths over K12)”.
    1. Drag the bar at the bottom edge of the track to resize it (100px here).
  4. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “pggb graph: segment carriage”.
    1. Track menu → Feature height → Collapsed
    2. Track menu → Show... → Labels → None
    3. Drag the bar at the bottom edge of the track to resize it (150px here).
    4. Track menu → Color by... → Attribute... → Edit as JSON...
  5. Type your region of interest into the location box and press Enter.This figure is at chr:1,299,300-1,300,900.

A figure adds its tracks to one session. The jbrowse CLI writes the same tracks into a config.json instead, where every session that opens it has them: add-track where flags cover the whole track, add-track-json where they do not.

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "K12_genes",
  "name": "K12 genes",
  "assemblyNames": [
    "K12"
  ],
  "adapter": {
    "type": "Gff3TabixAdapter",
    "gffGzLocation": {
      "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
    },
    "index": {
      "location": {
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
      }
    }
  }
}'

jbrowse add-track-json '{
  "type": "QuantitativeTrack",
  "trackId": "ecoli_pggb_depth",
  "name": "pggb graph: pangenome depth (paths over K12)",
  "assemblyNames": [
    "K12"
  ],
  "adapter": {
    "type": "BigWigAdapter",
    "bigWigLocation": {
      "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb_depth.bw"
    }
  }
}'

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "ecoli_pggb_carriage",
  "name": "pggb graph: segment carriage",
  "assemblyNames": [
    "K12"
  ],
  "adapter": {
    "type": "RgfaTabixAdapter",
    "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb"
  }
}'

Run these where the config.json is, or add --out <dir>, and point each uri at your own file. The config needs K12 already — jbrowse add-assembly adds yours. The location and the settings the steps carry are session state rather than track config — that half is the Spec tab, or jbrowse set-default-session.

This session spec draws the figure from test_data/graphgenomeview/config.json: paste it after &session=spec- on a JBrowse Web link that loads that config.

{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "K12_genes",
      "name": "K12 genes",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
          }
        }
      }
    },
    {
      "type": "QuantitativeTrack",
      "trackId": "ecoli_pggb_depth",
      "name": "pggb graph: pangenome depth (paths over K12)",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "BigWigAdapter",
        "bigWigLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb_depth.bw"
        }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_pggb_carriage",
      "name": "pggb graph: segment carriage",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb"
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:1,299,300-1,300,900",
      "tracks": [
        {
          "trackId": "K12_genes",
          "type": "LinearBasicDisplay",
          "height": 70
        },
        {
          "trackId": "ecoli_pggb_depth",
          "type": "LinearWiggleDisplay",
          "height": 100
        },
        {
          "trackId": "ecoli_pggb_carriage",
          "type": "LinearBasicDisplay",
          "displayMode": "collapsed",
          "showLabels": "none",
          "height": 150,
          "color": {
            "field": "carriers",
            "domain": [
              "5",
              "4",
              "3",
              "2",
              "1"
            ],
            "range": [
              "#bdbdbd",
              "#fed976",
              "#feb24c",
              "#fd8d3c",
              "#e31a1c"
            ],
            "labels": [
              "All 5 strains (core)",
              "4 strains",
              "3 strains",
              "2 strains",
              "1 strain (private)"
            ],
            "title": "Strains carrying"
          }
        }
      ]
    }
  ]
}

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "K12_genes",
      "name": "K12 genes",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
          }
        }
      }
    },
    {
      "type": "QuantitativeTrack",
      "trackId": "ecoli_pggb_depth",
      "name": "pggb graph: pangenome depth (paths over K12)",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "BigWigAdapter",
        "bigWigLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb_depth.bw"
        }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_pggb_carriage",
      "name": "pggb graph: segment carriage",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb"
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:1,299,300-1,300,900",
      "tracks": [
        {
          "trackId": "K12_genes",
          "type": "LinearBasicDisplay",
          "height": 70
        },
        {
          "trackId": "ecoli_pggb_depth",
          "type": "LinearWiggleDisplay",
          "height": 100
        },
        {
          "trackId": "ecoli_pggb_carriage",
          "type": "LinearBasicDisplay",
          "displayMode": "collapsed",
          "showLabels": "none",
          "height": 150,
          "color": {
            "field": "carriers",
            "domain": [
              "5",
              "4",
              "3",
              "2",
              "1"
            ],
            "range": [
              "#bdbdbd",
              "#fed976",
              "#feb24c",
              "#fd8d3c",
              "#e31a1c"
            ],
            "labels": [
              "All 5 strains (core)",
              "4 strains",
              "3 strains",
              "2 strains",
              "1 strain (private)"
            ],
            "title": "Strains carrying"
          }
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/graphgenomeview/config.json \
  --width 1000 --height 610 \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

This lane is one box per segment, unlike the depth track's windowed mean.

Opening a node in the strain that carries it

A segment the reference never visits sits on the strain's own coordinates. Right-click the 75 bp CFT073 segment and pick Open in CFT073: it opens CFT073 at 1,048,515 with its gene track.

The node's menu opened on the CFT073 allele, and the view its Open in entry adds: CFT073 in CFT073 coordinates, with its gene track already under it. Open the session this video starts in ↗

Open the session the video starts in ↗, then take the steps it shows:

  1. Open this allele on the CFT073 assembly

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session.

Nothing happens?

Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=test_data%2Fgraphgenomeview%2Fecoli_pangenome.json&session=spec-%7B%22sessionTracks%22%3A%5B%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22ecoli_pggb_segments%22%2C%22name%22%3A%22pggb+graph+segments+%28whole+graph%2C+by+locus%29%22%2C%22assemblyNames%22%3A%5B%22K12%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22RgfaTabixAdapter%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fecoli_pggb%22%2C%22coarse%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fecoli_pggb.tier50%22%2C%22aboveBpPerPx%22%3A1%7D%7D%7D%5D%2C%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22K12%22%2C%22loc%22%3A%22chr%3A1%2C004%2C500-1%2C004%2C961%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22ecoli_pggb_segments%22%2C%22type%22%3A%22LinearGraphDisplay%22%2C%22layoutMode%22%3A%22force%22%2C%22colorScheme%22%3A%22stable-rank%22%2C%22maxRegionBp%22%3A508%2C%22showBubbles%22%3Afalse%2C%22height%22%3A420%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+pangenome%2Fpggb_out_to_strain

With your own data, the steps behind the figure:

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “pggb graph segments (whole graph, by locus)”.
    1. Track menu → Layout → Force-directed layout
    2. Track menu → Color → Stable rank
    3. Track menu → Mark bubbles (unchecked)
    4. Drag the bar at the bottom edge of the track to resize it (420px here).
  3. Type your region of interest into the location box and press Enter.This figure is at chr:1,004,500-1,004,961.

Some settings have no written step yet — see the Spec tab.

Open this view in JBrowse Web ↗

Its genome and tracks are hosted, so File → Open track... there adds your own files beside them.

With your own data, the steps behind the figure:

  1. Put your genome in your JBrowse Web's config.json: jbrowse add-assembly adds it.This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “pggb graph segments (whole graph, by locus)”.
    1. Track menu → Layout → Force-directed layout
    2. Track menu → Color → Stable rank
    3. Track menu → Mark bubbles (unchecked)
    4. Drag the bar at the bottom edge of the track to resize it (420px here).
  3. Type your region of interest into the location box and press Enter.This figure is at chr:1,004,500-1,004,961.

Some settings have no written step yet — see the Spec tab.

A figure adds its tracks to one session. The jbrowse CLI writes the same tracks into a config.json instead, where every session that opens it has them: add-track where flags cover the whole track, add-track-json where they do not.

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "ecoli_pggb_segments",
  "name": "pggb graph segments (whole graph, by locus)",
  "assemblyNames": [
    "K12"
  ],
  "adapter": {
    "type": "RgfaTabixAdapter",
    "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb",
    "coarse": {
      "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50",
      "aboveBpPerPx": 1
    }
  }
}'

Run these where the config.json is, or add --out <dir>, and point each uri at your own file. The config needs K12 already — jbrowse add-assembly adds yours. The location and the settings the steps carry are session state rather than track config — that half is the Spec tab, or jbrowse set-default-session.

This session spec draws the figure from test_data/graphgenomeview/ecoli_pangenome.json: paste it after &session=spec- on a JBrowse Web link that loads that config.

{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_pggb_segments",
      "name": "pggb graph segments (whole graph, by locus)",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb",
        "coarse": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50",
          "aboveBpPerPx": 1
        }
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:1,004,500-1,004,961",
      "tracks": [
        {
          "trackId": "ecoli_pggb_segments",
          "type": "LinearGraphDisplay",
          "layoutMode": "force",
          "colorScheme": "stable-rank",
          "maxRegionBp": 508,
          "showBubbles": false,
          "height": 420
        }
      ]
    }
  ]
}

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_pggb_segments",
      "name": "pggb graph segments (whole graph, by locus)",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb",
        "coarse": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50",
          "aboveBpPerPx": 1
        }
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:1,004,500-1,004,961",
      "tracks": [
        {
          "trackId": "ecoli_pggb_segments",
          "type": "LinearGraphDisplay",
          "layoutMode": "force",
          "colorScheme": "stable-rank",
          "maxRegionBp": 508,
          "showBubbles": false,
          "height": 420
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/graphgenomeview/ecoli_pangenome.json \
  --width 1920 --height 1000 \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

K12 carries several genes in the span; CFT073 runs ssuE straight into pyrD with none between.

K12 above, with the span the 75 bp CFT073 segment bypasses boxed in blue; that segment ringed in the graph; and the view its Open in CFT073 entry adds below, where the same segment (boxed in red) sits between ssuE and pyrD with no genes between them. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session.

Nothing happens?

Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=test_data%2Fgraphgenomeview%2Fecoli_pangenome.json&session=spec-%7B%22sessionTracks%22%3A%5B%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22ecoli_pggb_segments%22%2C%22name%22%3A%22pggb+graph+segments+%28whole+graph%2C+by+locus%29%22%2C%22assemblyNames%22%3A%5B%22K12%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22RgfaTabixAdapter%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fecoli_pggb%22%2C%22coarse%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fecoli_pggb.tier50%22%2C%22aboveBpPerPx%22%3A1%7D%7D%7D%5D%2C%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22K12%22%2C%22loc%22%3A%22chr%3A996%2C800-1%2C005%2C900%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22K12_genes%22%2C%22type%22%3A%22LinearBasicDisplay%22%7D%5D%7D%2C%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22K12%22%2C%22loc%22%3A%22chr%3A1%2C004%2C500-1%2C004%2C961%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22ecoli_pggb_segments%22%2C%22type%22%3A%22LinearGraphDisplay%22%2C%22layoutMode%22%3A%22force%22%2C%22colorScheme%22%3A%22stable-rank%22%2C%22maxRegionBp%22%3A508%2C%22showBubbles%22%3Afalse%2C%22height%22%3A420%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+pangenome%2Fpggb_strain_launch

With your own data, the steps behind the figure:

  1. Open pane 1: Add → Linear genome view.
    1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
    2. Add your own track: open this view's track selector, click + and choose Add track, then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “K12 genes”.
    3. Type your region of interest into the location box and press Enter.This figure is at chr:996,800-1,005,900.
  2. Open pane 2: Add → Linear genome view.
    1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
    2. Add your own track: open this view's track selector, click + and choose Add track, then paste a URL or choose a local file.This figure uses “pggb graph segments (whole graph, by locus)”.
      1. Track menu → Layout → Force-directed layout
      2. Track menu → Color → Stable rank
      3. Track menu → Mark bubbles (unchecked)
      4. Drag the bar at the bottom edge of the track to resize it (420px here).
    3. Type your region of interest into the location box and press Enter.This figure is at chr:1,004,500-1,004,961.

Some settings have no written step yet — see the Spec tab.

Open this view in JBrowse Web ↗

Its genome and tracks are hosted, so File → Open track... there adds your own files beside them.

With your own data, the steps behind the figure:

  1. Open pane 1: Add → Linear genome view.
    1. Put your genome in your JBrowse Web's config.json: jbrowse add-assembly adds it.This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
    2. Add your own track: open this view's track selector, click + and choose Add track, then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “K12 genes”.
    3. Type your region of interest into the location box and press Enter.This figure is at chr:996,800-1,005,900.
  2. Open pane 2: Add → Linear genome view.
    1. Put your genome in your JBrowse Web's config.json: jbrowse add-assembly adds it.This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
    2. Add your own track: open this view's track selector, click + and choose Add track, then paste a URL or choose a local file.This figure uses “pggb graph segments (whole graph, by locus)”.
      1. Track menu → Layout → Force-directed layout
      2. Track menu → Color → Stable rank
      3. Track menu → Mark bubbles (unchecked)
      4. Drag the bar at the bottom edge of the track to resize it (420px here).
    3. Type your region of interest into the location box and press Enter.This figure is at chr:1,004,500-1,004,961.

Some settings have no written step yet — see the Spec tab.

A figure adds its tracks to one session. The jbrowse CLI writes the same tracks into a config.json instead, where every session that opens it has them: add-track where flags cover the whole track, add-track-json where they do not.

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "ecoli_pggb_segments",
  "name": "pggb graph segments (whole graph, by locus)",
  "assemblyNames": [
    "K12"
  ],
  "adapter": {
    "type": "RgfaTabixAdapter",
    "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb",
    "coarse": {
      "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50",
      "aboveBpPerPx": 1
    }
  }
}'

Run these where the config.json is, or add --out <dir>, and point each uri at your own file. The config needs K12 already — jbrowse add-assembly adds yours. The location and the settings the steps carry are session state rather than track config — that half is the Spec tab, or jbrowse set-default-session.

This session spec draws the figure from test_data/graphgenomeview/ecoli_pangenome.json: paste it after &session=spec- on a JBrowse Web link that loads that config.

{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_pggb_segments",
      "name": "pggb graph segments (whole graph, by locus)",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb",
        "coarse": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50",
          "aboveBpPerPx": 1
        }
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:996,800-1,005,900",
      "tracks": [
        {
          "trackId": "K12_genes",
          "type": "LinearBasicDisplay"
        }
      ]
    },
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:1,004,500-1,004,961",
      "tracks": [
        {
          "trackId": "ecoli_pggb_segments",
          "type": "LinearGraphDisplay",
          "layoutMode": "force",
          "colorScheme": "stable-rank",
          "maxRegionBp": 508,
          "showBubbles": false,
          "height": 420
        }
      ]
    }
  ]
}

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_pggb_segments",
      "name": "pggb graph segments (whole graph, by locus)",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb",
        "coarse": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50",
          "aboveBpPerPx": 1
        }
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:996,800-1,005,900",
      "tracks": [
        {
          "trackId": "K12_genes",
          "type": "LinearBasicDisplay"
        }
      ]
    },
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:1,004,500-1,004,961",
      "tracks": [
        {
          "trackId": "ecoli_pggb_segments",
          "type": "LinearGraphDisplay",
          "layoutMode": "force",
          "colorScheme": "stable-rank",
          "maxRegionBp": 508,
          "showBubbles": false,
          "height": 420
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/graphgenomeview/ecoli_pangenome.json \
  --width 1100 --height 1180 \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

The graph genome view guide covers the rest of the node's menu.

Limits of the locus index

Three limits on browsing a base-level graph by locus:

  • The index is offline. It is rebuilt whenever the graph changes.
  • Index size tracks total sequence. Prefer the SV-resolution minigraph graph for whole-genome browsing on a human pangenome, as the HPRC tutorial does.
  • A cut of segments covers a small window. The track declines past its node budget; a wider window is the tier's.

The build script also runs minigraph -cxggs and indexes its rGFA the same way, so the figure below puts one locus through both graphs.

One stretch of K12 at the colanic acid cluster through both graphs, each over the window it can draw. Left, the minigraph rGFA. Right, the pggb graph, with a node at every variant. Open in JBrowse: minigraph ↗ (large dataset — this session takes a while to load) · pggb ↗ (large dataset — this session takes a while to load)

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session.

Nothing happens?

Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=test_data%2Fgraphgenomeview%2Fconfig.json&session=spec-%7B%22sessionTracks%22%3A%5B%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22K12_genes%22%2C%22name%22%3A%22K12+genes%22%2C%22assemblyNames%22%3A%5B%22K12%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22Gff3TabixAdapter%22%2C%22gffGzLocation%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2FK12.gff.gz%22%7D%2C%22index%22%3A%7B%22location%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2FK12.gff.gz.tbi%22%7D%7D%7D%7D%2C%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22ecoli_minigraph_segments%22%2C%22name%22%3A%22minigraph+graph+segments+%28rGFA%29%22%2C%22assemblyNames%22%3A%5B%22K12%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22RgfaTabixAdapter%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fecoli_minigraph%22%7D%2C%22displayDefaults%22%3A%7B%22color%22%3A%22jexl%3Aget%28feature%2C%27rank%27%29%3D%3D0%3F%27rgb%2852%2C152%2C219%29%27%3A%27rgb%28237%2C137%2C44%29%27%22%7D%7D%5D%2C%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22K12%22%2C%22loc%22%3A%22chr%3A2118647-2139486%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22K12_genes%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22height%22%3A70%7D%2C%7B%22trackId%22%3A%22ecoli_minigraph_segments%22%2C%22type%22%3A%22LinearGraphDisplay%22%2C%22layoutMode%22%3A%22force%22%2C%22colorScheme%22%3A%22reference-position%22%2C%22colorDomain%22%3A%7B%22start%22%3A2118405%2C%22end%22%3A2146600%7D%2C%22maxRegionBp%22%3A22925%2C%22bubbleSpread%22%3A%22compress%22%2C%22layoutQuality%22%3A3%2C%22height%22%3A600%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+pangenome%2Fgraph_resolution_minigraph

With your own data, the steps behind the figure:

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “K12 genes”.
    1. Drag the bar at the bottom edge of the track to resize it (70px here).
  3. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “minigraph graph segments (rGFA)”.
    1. Track menu → Layout → Force-directed layout
    2. Track menu → Color → Reference position
    3. Track menu → Settings → Bubble spread → Compress lengthsSets a floor on how long a node is drawn in the force layout, so a short allele is a visible arm rather than a speck. Does nothing in the anchored layouts, which place a node from its coordinates.
    4. Track menu → Settings → Layout quality → HighHow many iterations the force layout runs. The default is enough for a small graph; raising it is what removes crossings from a drawing that has any.
    5. Drag the bar at the bottom edge of the track to resize it (600px here).
  4. Type your region of interest into the location box and press Enter.This figure is at chr:2118647-2139486.

Some settings have no written step yet — see the Spec tab.

Open this view in JBrowse Web ↗

Its genome and tracks are hosted, so File → Open track... there adds your own files beside them.

With your own data, the steps behind the figure:

  1. Put your genome in your JBrowse Web's config.json: jbrowse add-assembly adds it.This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “K12 genes”.
    1. Drag the bar at the bottom edge of the track to resize it (70px here).
  3. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “minigraph graph segments (rGFA)”.
    1. Track menu → Layout → Force-directed layout
    2. Track menu → Color → Reference position
    3. Track menu → Settings → Bubble spread → Compress lengthsSets a floor on how long a node is drawn in the force layout, so a short allele is a visible arm rather than a speck. Does nothing in the anchored layouts, which place a node from its coordinates.
    4. Track menu → Settings → Layout quality → HighHow many iterations the force layout runs. The default is enough for a small graph; raising it is what removes crossings from a drawing that has any.
    5. Drag the bar at the bottom edge of the track to resize it (600px here).
  4. Type your region of interest into the location box and press Enter.This figure is at chr:2118647-2139486.

Some settings have no written step yet — see the Spec tab.

A figure adds its tracks to one session. The jbrowse CLI writes the same tracks into a config.json instead, where every session that opens it has them: add-track where flags cover the whole track, add-track-json where they do not.

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "K12_genes",
  "name": "K12 genes",
  "assemblyNames": [
    "K12"
  ],
  "adapter": {
    "type": "Gff3TabixAdapter",
    "gffGzLocation": {
      "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
    },
    "index": {
      "location": {
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
      }
    }
  }
}'

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "ecoli_minigraph_segments",
  "name": "minigraph graph segments (rGFA)",
  "assemblyNames": [
    "K12"
  ],
  "adapter": {
    "type": "RgfaTabixAdapter",
    "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_minigraph"
  },
  "displayDefaults": {
    "color": "jexl:get(feature,'\''rank'\'')==0?'\''rgb(52,152,219)'\'':'\''rgb(237,137,44)'\''"
  }
}'

Run these where the config.json is, or add --out <dir>, and point each uri at your own file. The config needs K12 already — jbrowse add-assembly adds yours. The location and the settings the steps carry are session state rather than track config — that half is the Spec tab, or jbrowse set-default-session.

This session spec draws the figure from test_data/graphgenomeview/config.json: paste it after &session=spec- on a JBrowse Web link that loads that config.

{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "K12_genes",
      "name": "K12 genes",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
          }
        }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_minigraph_segments",
      "name": "minigraph graph segments (rGFA)",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_minigraph"
      },
      "displayDefaults": {
        "color": "jexl:get(feature,'rank')==0?'rgb(52,152,219)':'rgb(237,137,44)'"
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:2118647-2139486",
      "tracks": [
        {
          "trackId": "K12_genes",
          "type": "LinearBasicDisplay",
          "height": 70
        },
        {
          "trackId": "ecoli_minigraph_segments",
          "type": "LinearGraphDisplay",
          "layoutMode": "force",
          "colorScheme": "reference-position",
          "colorDomain": {
            "start": 2118405,
            "end": 2146600
          },
          "maxRegionBp": 22925,
          "bubbleSpread": "compress",
          "layoutQuality": 3,
          "height": 600
        }
      ]
    }
  ]
}

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "K12_genes",
      "name": "K12 genes",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
          }
        }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_minigraph_segments",
      "name": "minigraph graph segments (rGFA)",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_minigraph"
      },
      "displayDefaults": {
        "color": "jexl:get(feature,'rank')==0?'rgb(52,152,219)':'rgb(237,137,44)'"
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:2118647-2139486",
      "tracks": [
        {
          "trackId": "K12_genes",
          "type": "LinearBasicDisplay",
          "height": 70
        },
        {
          "trackId": "ecoli_minigraph_segments",
          "type": "LinearGraphDisplay",
          "layoutMode": "force",
          "colorScheme": "reference-position",
          "colorDomain": {
            "start": 2118405,
            "end": 2146600
          },
          "maxRegionBp": 22925,
          "bubbleSpread": "compress",
          "layoutQuality": 3,
          "height": 600
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/graphgenomeview/config.json \
  --width 750 --height 940 \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session.

Nothing happens?

Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=test_data%2Fgraphgenomeview%2Fconfig.json&session=spec-%7B%22sessionTracks%22%3A%5B%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22K12_genes%22%2C%22name%22%3A%22K12+genes%22%2C%22assemblyNames%22%3A%5B%22K12%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22Gff3TabixAdapter%22%2C%22gffGzLocation%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2FK12.gff.gz%22%7D%2C%22index%22%3A%7B%22location%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2FK12.gff.gz.tbi%22%7D%7D%7D%7D%2C%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22ecoli_pggb_segments%22%2C%22name%22%3A%22pggb+graph+segments+%28whole+graph%2C+by+locus%29%22%2C%22assemblyNames%22%3A%5B%22K12%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22RgfaTabixAdapter%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fecoli_pggb%22%2C%22coarse%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fecoli_pggb.tier50%22%2C%22aboveBpPerPx%22%3A1%7D%7D%7D%5D%2C%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22K12%22%2C%22loc%22%3A%22chr%3A2120001-2120300%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22K12_genes%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22height%22%3A70%7D%2C%7B%22trackId%22%3A%22ecoli_pggb_segments%22%2C%22type%22%3A%22LinearGraphDisplay%22%2C%22layoutMode%22%3A%22force%22%2C%22colorScheme%22%3A%22reference-position%22%2C%22colorDomain%22%3A%7B%22start%22%3A2118405%2C%22end%22%3A2146600%7D%2C%22maxRegionBp%22%3A330%2C%22bubbleSpread%22%3A%22compress%22%2C%22layoutQuality%22%3A3%2C%22height%22%3A600%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+pangenome%2Fgraph_resolution_pggb

With your own data, the steps behind the figure:

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “K12 genes”.
    1. Drag the bar at the bottom edge of the track to resize it (70px here).
  3. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “pggb graph segments (whole graph, by locus)”.
    1. Track menu → Layout → Force-directed layout
    2. Track menu → Color → Reference position
    3. Track menu → Settings → Bubble spread → Compress lengthsSets a floor on how long a node is drawn in the force layout, so a short allele is a visible arm rather than a speck. Does nothing in the anchored layouts, which place a node from its coordinates.
    4. Track menu → Settings → Layout quality → HighHow many iterations the force layout runs. The default is enough for a small graph; raising it is what removes crossings from a drawing that has any.
    5. Drag the bar at the bottom edge of the track to resize it (600px here).
  4. Type your region of interest into the location box and press Enter.This figure is at chr:2120001-2120300.

Some settings have no written step yet — see the Spec tab.

Open this view in JBrowse Web ↗

Its genome and tracks are hosted, so File → Open track... there adds your own files beside them.

With your own data, the steps behind the figure:

  1. Put your genome in your JBrowse Web's config.json: jbrowse add-assembly adds it.This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “K12 genes”.
    1. Drag the bar at the bottom edge of the track to resize it (70px here).
  3. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “pggb graph segments (whole graph, by locus)”.
    1. Track menu → Layout → Force-directed layout
    2. Track menu → Color → Reference position
    3. Track menu → Settings → Bubble spread → Compress lengthsSets a floor on how long a node is drawn in the force layout, so a short allele is a visible arm rather than a speck. Does nothing in the anchored layouts, which place a node from its coordinates.
    4. Track menu → Settings → Layout quality → HighHow many iterations the force layout runs. The default is enough for a small graph; raising it is what removes crossings from a drawing that has any.
    5. Drag the bar at the bottom edge of the track to resize it (600px here).
  4. Type your region of interest into the location box and press Enter.This figure is at chr:2120001-2120300.

Some settings have no written step yet — see the Spec tab.

A figure adds its tracks to one session. The jbrowse CLI writes the same tracks into a config.json instead, where every session that opens it has them: add-track where flags cover the whole track, add-track-json where they do not.

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "K12_genes",
  "name": "K12 genes",
  "assemblyNames": [
    "K12"
  ],
  "adapter": {
    "type": "Gff3TabixAdapter",
    "gffGzLocation": {
      "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
    },
    "index": {
      "location": {
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
      }
    }
  }
}'

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "ecoli_pggb_segments",
  "name": "pggb graph segments (whole graph, by locus)",
  "assemblyNames": [
    "K12"
  ],
  "adapter": {
    "type": "RgfaTabixAdapter",
    "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb",
    "coarse": {
      "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50",
      "aboveBpPerPx": 1
    }
  }
}'

Run these where the config.json is, or add --out <dir>, and point each uri at your own file. The config needs K12 already — jbrowse add-assembly adds yours. The location and the settings the steps carry are session state rather than track config — that half is the Spec tab, or jbrowse set-default-session.

This session spec draws the figure from test_data/graphgenomeview/config.json: paste it after &session=spec- on a JBrowse Web link that loads that config.

{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "K12_genes",
      "name": "K12 genes",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
          }
        }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_pggb_segments",
      "name": "pggb graph segments (whole graph, by locus)",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb",
        "coarse": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50",
          "aboveBpPerPx": 1
        }
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:2120001-2120300",
      "tracks": [
        {
          "trackId": "K12_genes",
          "type": "LinearBasicDisplay",
          "height": 70
        },
        {
          "trackId": "ecoli_pggb_segments",
          "type": "LinearGraphDisplay",
          "layoutMode": "force",
          "colorScheme": "reference-position",
          "colorDomain": {
            "start": 2118405,
            "end": 2146600
          },
          "maxRegionBp": 330,
          "bubbleSpread": "compress",
          "layoutQuality": 3,
          "height": 600
        }
      ]
    }
  ]
}

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "K12_genes",
      "name": "K12 genes",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
          }
        }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_pggb_segments",
      "name": "pggb graph segments (whole graph, by locus)",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb",
        "coarse": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.tier50",
          "aboveBpPerPx": 1
        }
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:2120001-2120300",
      "tracks": [
        {
          "trackId": "K12_genes",
          "type": "LinearBasicDisplay",
          "height": 70
        },
        {
          "trackId": "ecoli_pggb_segments",
          "type": "LinearGraphDisplay",
          "layoutMode": "force",
          "colorScheme": "reference-position",
          "colorDomain": {
            "start": 2118405,
            "end": 2146600
          },
          "maxRegionBp": 330,
          "bubbleSpread": "compress",
          "layoutQuality": 3,
          "height": 600
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/graphgenomeview/config.json \
  --width 750 --height 940 \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

Browse the rGFA whole-genome, and open the pggb graph for every base.

A window as a file

With no index, Add → Graph genome view takes a GFA by file or URL. Three odgi commands cut one:

-E is the aggressive option; -c/-d expand by a bounded number of steps or bp instead:

in_pggb bash -c "odgi extract -i /data/$og -r K12#1#chr:1004500-1004900 -E -o - \
  | odgi sort -i - -o - -O \
  | odgi view -i - -g" > ecoli_pggb_subgraph.gfa

A plain GFA marks no path as the reference, so pick one under View menu → Settings → Reference path.

The same odgi extract/sort/view walk, run outside the browser, puts those nodes on a linear track:

curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/gfa_nodes_to_bed.py
python3 gfa_nodes_to_bed.py ecoli_pggb_subgraph.gfa K12#1#chr chr \
  | sort -k1,1 -k2,2n | bgzip > ecoli_pggb_subgraph_nodes.bed.gz
tabix -p bed ecoli_pggb_subgraph_nodes.bed.gz

The BED's itemRgb is the view's own viridis Depth ramp, needing no color configuration.

A cut graph has ends: the ringed node marks where CFT073 rejoins after the same deletion, one end open since its far link falls outside. -c 1 fetches only that anchor, skipping the nodes between.

The same deletion is four nodes in the minigraph graph:

tabix https://jbrowse.org/demos/ecoli_pangenome/ecoli_minigraph.links.bed.gz \
  'K12#1#chr:997000-1005000'

s378 → s379 → s380 is K12 through the deletion; s378 → s2025 → s380 is CFT073 around it.

The extracted file beside a linear view of the same locus, anchored on the graph's K12 path so both share an axis and the Depth colors. The ringed node is the one left with an open end. Open this view in JBrowse ↗

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session.

Nothing happens?

Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=test_data%2Fgraphgenomeview%2Fconfig.json&session=spec-%7B%22sessionTracks%22%3A%5B%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22K12_genes%22%2C%22name%22%3A%22K12+genes%22%2C%22assemblyNames%22%3A%5B%22K12%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22Gff3TabixAdapter%22%2C%22gffGzLocation%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2FK12.gff.gz%22%7D%2C%22index%22%3A%7B%22location%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2FK12.gff.gz.tbi%22%7D%7D%7D%7D%2C%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22ecoli_pggb_subgraph_nodes%22%2C%22name%22%3A%22pggb+subgraph%3A+nodes+on+K12%2C+colored+by+depth%22%2C%22assemblyNames%22%3A%5B%22K12%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22BedTabixAdapter%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fecoli_pggb_subgraph_nodes.bed.gz%22%2C%22columnNames%22%3A%5B%22chrom%22%2C%22start%22%2C%22end%22%2C%22name%22%2C%22depth%22%2C%22strand%22%2C%22thickStart%22%2C%22thickEnd%22%2C%22itemRgb%22%5D%7D%7D%5D%2C%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22K12%22%2C%22loc%22%3A%22chr%3A1%2C004%2C450-1%2C005%2C010%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22ecoli_pggb_subgraph_nodes%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22displayMode%22%3A%22collapsed%22%2C%22height%22%3A40%7D%2C%7B%22trackId%22%3A%22K12_genes%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22height%22%3A60%2C%22color%22%3A%22rgb%28130%2C130%2C130%29%22%7D%5D%7D%2C%7B%22type%22%3A%22GraphGenomeView%22%2C%22gfaLocation%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fecoli_pggb_subgraph.gfa%22%7D%2C%22colorScheme%22%3A%22depth%22%2C%22layoutMode%22%3A%22auto%22%2C%22referencePath%22%3A%22K12%22%2C%22showBubbles%22%3Afalse%7D%5D%7D&sessionName=JBrowse+docs%3A+pangenome%2Flocal_subgraph

With your own data, the steps behind the figure:

  1. Open pane 1: Add → Linear genome view.
    1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
    2. Add your own track: open this view's track selector, click + and choose Add track, then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed BED (.bed.gz + .tbi).This figure uses “pggb subgraph: nodes on K12, colored by depth”.
      1. Track menu → Feature height → Collapsed
      2. Drag the bar at the bottom edge of the track to resize it (40px here).
    3. Add your own track: open this view's track selector, click + and choose Add track, then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “K12 genes”.
      1. Drag the bar at the bottom edge of the track to resize it (60px here).
      2. Track menu → Color by... → Solid color... → rgb(130,130,130)
    4. Type your region of interest into the location box and press Enter.This figure is at chr:1,004,450-1,005,010.
  2. Pane 2
    1. Open the view: Add → Graph genome view, then on its "Load a GFA graph" form paste the URL and click Open (or Choose file for a local .gfa)Loads the whole graph, so it suits a subgraph or a small assembly. A window of a large one is cut from a segments track instead.
    2. Graph view toolbar → Color → Depth
    3. Graph view toolbar → Layout → Anchored
    4. Graph view menu → Settings → Reference path → K12Which path the anchored layouts draw x against. Only offered when the file states more than one.
    5. Graph view menu → Settings → Mark bubbles (unchecked)

Open this view in JBrowse Web ↗

Its genome and tracks are hosted, so File → Open track... there adds your own files beside them.

With your own data, the steps behind the figure:

  1. Open pane 1: Add → Linear genome view.
    1. Put your genome in your JBrowse Web's config.json: jbrowse add-assembly adds it.This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
    2. Add your own track: open this view's track selector, click + and choose Add track, then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed BED (.bed.gz + .tbi).This figure uses “pggb subgraph: nodes on K12, colored by depth”.
      1. Track menu → Feature height → Collapsed
      2. Drag the bar at the bottom edge of the track to resize it (40px here).
    3. Add your own track: open this view's track selector, click + and choose Add track, then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “K12 genes”.
      1. Drag the bar at the bottom edge of the track to resize it (60px here).
      2. Track menu → Color by... → Solid color... → rgb(130,130,130)
    4. Type your region of interest into the location box and press Enter.This figure is at chr:1,004,450-1,005,010.
  2. Pane 2
    1. Open the view: Add → Graph genome view, then on its "Load a GFA graph" form paste the URL and click Open (or Choose file for a local .gfa)Loads the whole graph, so it suits a subgraph or a small assembly. A window of a large one is cut from a segments track instead.
    2. Graph view toolbar → Color → Depth
    3. Graph view toolbar → Layout → Anchored
    4. Graph view menu → Settings → Reference path → K12Which path the anchored layouts draw x against. Only offered when the file states more than one.
    5. Graph view menu → Settings → Mark bubbles (unchecked)

A figure adds its tracks to one session. The jbrowse CLI writes the same tracks into a config.json instead, where every session that opens it has them: add-track where flags cover the whole track, add-track-json where they do not.

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "K12_genes",
  "name": "K12 genes",
  "assemblyNames": [
    "K12"
  ],
  "adapter": {
    "type": "Gff3TabixAdapter",
    "gffGzLocation": {
      "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
    },
    "index": {
      "location": {
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
      }
    }
  }
}'

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "ecoli_pggb_subgraph_nodes",
  "name": "pggb subgraph: nodes on K12, colored by depth",
  "assemblyNames": [
    "K12"
  ],
  "adapter": {
    "type": "BedTabixAdapter",
    "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb_subgraph_nodes.bed.gz",
    "columnNames": [
      "chrom",
      "start",
      "end",
      "name",
      "depth",
      "strand",
      "thickStart",
      "thickEnd",
      "itemRgb"
    ]
  }
}'

Run these where the config.json is, or add --out <dir>, and point each uri at your own file. The config needs K12 already — jbrowse add-assembly adds yours. The location and the settings the steps carry are session state rather than track config — that half is the Spec tab, or jbrowse set-default-session.

This session spec draws the figure from test_data/graphgenomeview/config.json: paste it after &session=spec- on a JBrowse Web link that loads that config.

{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "K12_genes",
      "name": "K12 genes",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
          }
        }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_pggb_subgraph_nodes",
      "name": "pggb subgraph: nodes on K12, colored by depth",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "BedTabixAdapter",
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb_subgraph_nodes.bed.gz",
        "columnNames": [
          "chrom",
          "start",
          "end",
          "name",
          "depth",
          "strand",
          "thickStart",
          "thickEnd",
          "itemRgb"
        ]
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:1,004,450-1,005,010",
      "tracks": [
        {
          "trackId": "ecoli_pggb_subgraph_nodes",
          "type": "LinearBasicDisplay",
          "displayMode": "collapsed",
          "height": 40
        },
        {
          "trackId": "K12_genes",
          "type": "LinearBasicDisplay",
          "height": 60,
          "color": "rgb(130,130,130)"
        }
      ]
    },
    {
      "type": "GraphGenomeView",
      "gfaLocation": {
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb_subgraph.gfa"
      },
      "colorScheme": "depth",
      "layoutMode": "auto",
      "referencePath": "K12",
      "showBubbles": false
    }
  ]
}

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "K12_genes",
      "name": "K12 genes",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
          }
        }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "ecoli_pggb_subgraph_nodes",
      "name": "pggb subgraph: nodes on K12, colored by depth",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "BedTabixAdapter",
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb_subgraph_nodes.bed.gz",
        "columnNames": [
          "chrom",
          "start",
          "end",
          "name",
          "depth",
          "strand",
          "thickStart",
          "thickEnd",
          "itemRgb"
        ]
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:1,004,450-1,005,010",
      "tracks": [
        {
          "trackId": "ecoli_pggb_subgraph_nodes",
          "type": "LinearBasicDisplay",
          "displayMode": "collapsed",
          "height": 40
        },
        {
          "trackId": "K12_genes",
          "type": "LinearBasicDisplay",
          "height": 60,
          "color": "rgb(130,130,130)"
        }
      ]
    },
    {
      "type": "GraphGenomeView",
      "gfaLocation": {
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb_subgraph.gfa"
      },
      "colorScheme": "depth",
      "layoutMode": "auto",
      "referencePath": "K12",
      "showBubbles": false
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/graphgenomeview/config.json \
  --width 1000 --height 640 \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

-d is the answer at a collapsed repeat, where -E walks out to every copy: at the 16S rRNA gene rrsB, -d 500 keeps the cut to a handful of segments.

in_pggb bash -c "odgi extract -i /data/$og -r K12#1#chr:4166800-4167300 -d 500 -o - \
  | odgi sort -i - -o - -O \
  | odgi view -i - -g" > ecoli_pggb_rrna.gfa

odgi paths -L lists two copies each in Sakai, CFT073, NCTC86 and IAI39 and one in K12: the same collapse the depth curve reads as a spike and untangle draws in coordinate space.

Drawing the haplotype paths

A P line is a path through the graph; a W line is the same in GFA 1.1's walk syntax. View menu → Settings → Draw paths splits every node into one lane per path. Set Color to Grey first.

Neither an rGFA nor a subgraph cut from the tabix index carries P or W lines. The file route keeps them: cut the IS5 bubble the coarse tier arrows as a file.

in_pggb bash -c "odgi extract -i /data/$og -r K12#1#chr:1299400-1300800 -E -o - \
  | odgi sort -i - -o - -O \
  | odgi view -i - -g" > ecoli_pggb_is5.gfa

The gene lane names the element, insH21, the IS5 transposase, and the loop in the drawing below is its node.

The IS5 bubble cut as a file, so its P lines survive: the interval in K12 coordinates above, the bubble with the strain paths drawn below and Sakai picked in the Walk menu. The element's loop fades because Sakai's walk skips it, as the four MAF rows other than K12 do above. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session.

Nothing happens?

Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=test_data%2Fgraphgenomeview%2Fconfig.json&session=spec-%7B%22sessionTracks%22%3A%5B%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22K12_genes%22%2C%22name%22%3A%22K12+genes%22%2C%22assemblyNames%22%3A%5B%22K12%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22Gff3TabixAdapter%22%2C%22gffGzLocation%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2FK12.gff.gz%22%7D%2C%22index%22%3A%7B%22location%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2FK12.gff.gz.tbi%22%7D%7D%7D%7D%2C%7B%22type%22%3A%22MafTrack%22%2C%22trackId%22%3A%22ecoli_pggb_maf%22%2C%22name%22%3A%22pggb+graph%3A+whole-genome+alignment+%28MAF%2C+vs+K12%29%22%2C%22assemblyNames%22%3A%5B%22K12%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22MafTabixAdapter%22%2C%22samples%22%3A%5B%22K12%22%2C%22Sakai%22%2C%22CFT073%22%2C%22NCTC86%22%2C%22IAI39%22%5D%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fecoli_pggb.maf.bed.gz%22%7D%7D%5D%2C%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22displayName%22%3A%22The+same+1.4+kb+in+K12+coordinates%22%2C%22assembly%22%3A%22K12%22%2C%22loc%22%3A%22chr%3A1%2C299%2C300-1%2C300%2C900%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22K12_genes%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22height%22%3A70%7D%2C%7B%22trackId%22%3A%22ecoli_pggb_maf%22%2C%22type%22%3A%22LinearMafDisplay%22%2C%22rows%22%3A%7B%22domain%22%3A%5B%22K12%22%2C%22CFT073%22%2C%22IAI39%22%2C%22NCTC86%22%2C%22Sakai%22%5D%7D%2C%22showTree%22%3Atrue%2C%22height%22%3A150%7D%5D%7D%2C%7B%22type%22%3A%22GraphGenomeView%22%2C%22displayName%22%3A%22The+graph+over+that+interval%2C+colored+by+strain%22%2C%22gfaLocation%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fecoli_pangenome%2Fecoli_pggb_is5.gfa%22%7D%2C%22layoutMode%22%3A%22force%22%2C%22layoutQuality%22%3A4%2C%22bubbleSpread%22%3A%22open%22%2C%22colorScheme%22%3A%22grey%22%2C%22referencePath%22%3A%22K12%22%2C%22highlightedPath%22%3A%22Sakai%231%23chr%3A1743580-1743789%22%2C%22drawPaths%22%3Atrue%2C%22showBubbles%22%3Afalse%7D%5D%7D&sessionName=JBrowse+docs%3A+pangenome%2Fpggb_haplotype_paths

With your own data, the steps behind the figure:

  1. Open pane 1: Add → Linear genome view.
    1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
    2. Add your own track: open this view's track selector, click + and choose Add track, then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “K12 genes”.
      1. Drag the bar at the bottom edge of the track to resize it (70px here).
    3. Add your own track: open this view's track selector, click + and choose Add track, then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed MAF (.maf.gz + .tbi).This figure uses “pggb graph: whole-genome alignment (MAF, vs K12)”.
      1. Track menu → Edit colors/arrangement... → drag the rows into orderThe same dialog renames a row and recolors it, so a figure's 5 rows carry their order, any labels it shows, and any color it picked.
      2. Track menu → Show... → Show tree (checked)On by default. The item is disabled until there is a tree to show — a clustering run, or a MAF track’s guide tree; the row labels have their own toggle beneath it.
      3. Drag the bar at the bottom edge of the track to resize it (150px here).
    4. Type your region of interest into the location box and press Enter.This figure is at chr:1,299,300-1,300,900.
    5. Click the view's title in its header and enter "The same 1.4 kb in K12 coordinates"
  2. Pane 2
    1. Click the view's title in its header and enter "The graph over that interval, colored by strain"
    2. Open the view: Add → Graph genome view, then on its "Load a GFA graph" form paste the URL and click Open (or Choose file for a local .gfa)Loads the whole graph, so it suits a subgraph or a small assembly. A window of a large one is cut from a segments track instead.
    3. Graph view toolbar → Layout → Force-directed layout
    4. Graph view menu → Settings → Layout quality → HighestHow many iterations the force layout runs. The default is enough for a small graph; raising it is what removes crossings from a drawing that has any.
    5. Graph view menu → Settings → Bubble spread → Open bubblesSets a floor on how long a node is drawn in the force layout, so a short allele is a visible arm rather than a speck. Does nothing in the anchored layouts, which place a node from its coordinates.
    6. Graph view toolbar → Color → Grey
    7. Graph view menu → Settings → Reference path → K12Which path the anchored layouts draw x against. Only offered when the file states more than one.
    8. Graph view toolbar → Walk → Sakai#1#chr:1743580-1743789Lifts one walk out of the drawing and fades the rest. The menu names each walk by the shortest part of its name that tells it apart.
    9. Graph view menu → Settings → Draw paths (on)Colors every node and connector by the P/W records through it, one lane per path in legend order, so a path that skips a node leaves its lane empty. Needs a GFA that states its paths: an rGFA and an indexed cut both carry segments and links only.
    10. Graph view menu → Settings → Mark bubbles (unchecked)

Open this view in JBrowse Web ↗

Its genome and tracks are hosted, so File → Open track... there adds your own files beside them.

With your own data, the steps behind the figure:

  1. Open pane 1: Add → Linear genome view.
    1. Put your genome in your JBrowse Web's config.json: jbrowse add-assembly adds it.This figure uses K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
    2. Add your own track: open this view's track selector, click + and choose Add track, then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “K12 genes”.
      1. Drag the bar at the bottom edge of the track to resize it (70px here).
    3. Add your own track: open this view's track selector, click + and choose Add track, then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed MAF (.maf.gz + .tbi).This figure uses “pggb graph: whole-genome alignment (MAF, vs K12)”.
      1. Track menu → Edit colors/arrangement... → drag the rows into orderThe same dialog renames a row and recolors it, so a figure's 5 rows carry their order, any labels it shows, and any color it picked.
      2. Track menu → Show... → Show tree (checked)On by default. The item is disabled until there is a tree to show — a clustering run, or a MAF track’s guide tree; the row labels have their own toggle beneath it.
      3. Drag the bar at the bottom edge of the track to resize it (150px here).
    4. Type your region of interest into the location box and press Enter.This figure is at chr:1,299,300-1,300,900.
    5. Click the view's title in its header and enter "The same 1.4 kb in K12 coordinates"
  2. Pane 2
    1. Click the view's title in its header and enter "The graph over that interval, colored by strain"
    2. Open the view: Add → Graph genome view, then on its "Load a GFA graph" form paste the URL and click Open (or Choose file for a local .gfa)Loads the whole graph, so it suits a subgraph or a small assembly. A window of a large one is cut from a segments track instead.
    3. Graph view toolbar → Layout → Force-directed layout
    4. Graph view menu → Settings → Layout quality → HighestHow many iterations the force layout runs. The default is enough for a small graph; raising it is what removes crossings from a drawing that has any.
    5. Graph view menu → Settings → Bubble spread → Open bubblesSets a floor on how long a node is drawn in the force layout, so a short allele is a visible arm rather than a speck. Does nothing in the anchored layouts, which place a node from its coordinates.
    6. Graph view toolbar → Color → Grey
    7. Graph view menu → Settings → Reference path → K12Which path the anchored layouts draw x against. Only offered when the file states more than one.
    8. Graph view toolbar → Walk → Sakai#1#chr:1743580-1743789Lifts one walk out of the drawing and fades the rest. The menu names each walk by the shortest part of its name that tells it apart.
    9. Graph view menu → Settings → Draw paths (on)Colors every node and connector by the P/W records through it, one lane per path in legend order, so a path that skips a node leaves its lane empty. Needs a GFA that states its paths: an rGFA and an indexed cut both carry segments and links only.
    10. Graph view menu → Settings → Mark bubbles (unchecked)

A figure adds its tracks to one session. The jbrowse CLI writes the same tracks into a config.json instead, where every session that opens it has them: add-track where flags cover the whole track, add-track-json where they do not.

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "K12_genes",
  "name": "K12 genes",
  "assemblyNames": [
    "K12"
  ],
  "adapter": {
    "type": "Gff3TabixAdapter",
    "gffGzLocation": {
      "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
    },
    "index": {
      "location": {
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
      }
    }
  }
}'

jbrowse add-track-json '{
  "type": "MafTrack",
  "trackId": "ecoli_pggb_maf",
  "name": "pggb graph: whole-genome alignment (MAF, vs K12)",
  "assemblyNames": [
    "K12"
  ],
  "adapter": {
    "type": "MafTabixAdapter",
    "samples": [
      "K12",
      "Sakai",
      "CFT073",
      "NCTC86",
      "IAI39"
    ],
    "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.maf.bed.gz"
  }
}'

Run these where the config.json is, or add --out <dir>, and point each uri at your own file. The config needs K12 already — jbrowse add-assembly adds yours. The location and the settings the steps carry are session state rather than track config — that half is the Spec tab, or jbrowse set-default-session.

This session spec draws the figure from test_data/graphgenomeview/config.json: paste it after &session=spec- on a JBrowse Web link that loads that config.

{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "K12_genes",
      "name": "K12 genes",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
          }
        }
      }
    },
    {
      "type": "MafTrack",
      "trackId": "ecoli_pggb_maf",
      "name": "pggb graph: whole-genome alignment (MAF, vs K12)",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "MafTabixAdapter",
        "samples": [
          "K12",
          "Sakai",
          "CFT073",
          "NCTC86",
          "IAI39"
        ],
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.maf.bed.gz"
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "displayName": "The same 1.4 kb in K12 coordinates",
      "assembly": "K12",
      "loc": "chr:1,299,300-1,300,900",
      "tracks": [
        {
          "trackId": "K12_genes",
          "type": "LinearBasicDisplay",
          "height": 70
        },
        {
          "trackId": "ecoli_pggb_maf",
          "type": "LinearMafDisplay",
          "rows": {
            "domain": [
              "K12",
              "CFT073",
              "IAI39",
              "NCTC86",
              "Sakai"
            ]
          },
          "showTree": true,
          "height": 150
        }
      ]
    },
    {
      "type": "GraphGenomeView",
      "displayName": "The graph over that interval, colored by strain",
      "gfaLocation": {
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb_is5.gfa"
      },
      "layoutMode": "force",
      "layoutQuality": 4,
      "bubbleSpread": "open",
      "colorScheme": "grey",
      "referencePath": "K12",
      "highlightedPath": "Sakai#1#chr:1743580-1743789",
      "drawPaths": true,
      "showBubbles": false
    }
  ]
}

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "K12_genes",
      "name": "K12 genes",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi"
          }
        }
      }
    },
    {
      "type": "MafTrack",
      "trackId": "ecoli_pggb_maf",
      "name": "pggb graph: whole-genome alignment (MAF, vs K12)",
      "assemblyNames": [
        "K12"
      ],
      "adapter": {
        "type": "MafTabixAdapter",
        "samples": [
          "K12",
          "Sakai",
          "CFT073",
          "NCTC86",
          "IAI39"
        ],
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb.maf.bed.gz"
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "displayName": "The same 1.4 kb in K12 coordinates",
      "assembly": "K12",
      "loc": "chr:1,299,300-1,300,900",
      "tracks": [
        {
          "trackId": "K12_genes",
          "type": "LinearBasicDisplay",
          "height": 70
        },
        {
          "trackId": "ecoli_pggb_maf",
          "type": "LinearMafDisplay",
          "rows": {
            "domain": [
              "K12",
              "CFT073",
              "IAI39",
              "NCTC86",
              "Sakai"
            ]
          },
          "showTree": true,
          "height": 150
        }
      ]
    },
    {
      "type": "GraphGenomeView",
      "displayName": "The graph over that interval, colored by strain",
      "gfaLocation": {
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb_is5.gfa"
      },
      "layoutMode": "force",
      "layoutQuality": 4,
      "bubbleSpread": "open",
      "colorScheme": "grey",
      "referencePath": "K12",
      "highlightedPath": "Sakai#1#chr:1743580-1743789",
      "drawPaths": true,
      "showBubbles": false
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/graphgenomeview/config.json \
  --width 1000 --height 980 \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

With the paths in the file, the view derives the bubble under Mark bubbles; the Walk dropdown lifts one strain's path out of the drawing.

Reproduce it end to end

build_ecoli_pangenome_graph.sh runs everything above in one shot, fetching the helper scripts it needs:

curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/build_ecoli_pangenome_graph.sh
bash build_ecoli_pangenome_graph.sh   # builds ./ecoli_pangenome_graph_build/jbrowse2
npx --yes serve ecoli_pangenome_graph_build/jbrowse2

In one run it:

  • downloads the RefSeq genomes and runs pggb
  • converts the projections above from the wfmash PAF, odgi untangle, both VCF tiers, the MAF, odgi similarity, odgi depth and odgi pav
  • downloads JBrowse and writes a config.json with the assemblies, gene tracks, graph-derived tracks, and a default session
  • writes the odgi viz raster, every cut GFA this page opens as a file, and the rGFA tabix indexes behind the segments track

The config.json declares the graph genome view plugin; force the container runtime with CONTAINER=singularity. JBrowse Desktop opens the folder's config.json by path, so npx serve is only for the web build.

Adding genomes to the strain table is the only edit an expanded pangenome needs; wfmash mapping cost grows with the square of the genome count.

See also