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Synteny visualization (pairwise minimap2)

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.10. Desktop beta builds are coming soon.

Align two assemblies with minimap2 -c --eqx, load the PAF as a synteny track, and read it whole-genome in a dotplot and base-level in the linear synteny view. add-track -a takes query,target, the reverse of the minimap2 argument order.

Prerequisites

  • a JBrowse 2 instance (see the web quickstart, or the desktop quickstart; the steps below are identical on both, and on Desktop the alignments are local files)
  • minimap2
  • python3, which the build script uses to copy the hub configs
  • node, for the JBrowse CLI

On Debian/Ubuntu, apt install minimap2 covers the aligner, and node comes from nodejs.org.

Where the data comes from

Three H. pylori RefSeq assemblies and their genome hubs on genomes.jbrowse.org (26695, CHC155, J99). Each hub serves the sequence minimap2 aligns and a config holding the assembly and its NCBI RefSeq genes.

Three strains, stacked

Three Helicobacter pylori strains (26695, CHC155, and J99) go from their genome hubs to a stacked three-genome synteny view. The steps work the same on any pair of assemblies.

Aligning the assemblies

minimap2 -c -x asm20 --eqx hpylori_j99.fa.gz hpylori_26695.fa.gz > 26695_vs_j99.paf
  • -x asm20 is the assembly preset for the divergence between the genomes. asm5 covers up to about 5%; these strains diverge well past that.
  • -c emits the base-level CIGAR the linear synteny view draws from.
  • --eqx splits CIGAR matches (=) from mismatches (X), so the same track opened in a plain linear genome view draws per-base mismatches. Color by value → Identity reads the PAF's divergence tag or match counts.

JBrowse also loads MUMmer .delta and UCSC .chain files directly, and paftools.js has delta2paf and chain2paf for converting them.

Loading the assemblies and the alignment

Each strain's hub config.json holds a whole JBrowse assembly: the 2bit sequence, an alias table and the NCBI RefSeq gene track. The build copies each assembly entry and gene track into its own config as the hub wrote it, relabels the row, and adds the old short name as an alias so a session can still say hpylori_26695:

{
  "name": "GCF_000307795.1",
  "displayName": "H. pylori 26695",
  "aliases": ["hpylori_26695"],
  "sequence": {
    "type": "ReferenceSequenceTrack",
    "trackId": "GCF_000307795.1-ReferenceSequenceTrack",
    "adapter": {
      "type": "TwoBitAdapter",
      "uri": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/307/795/GCF_000307795.1/GCF_000307795.1.2bit",
      "chromSizes": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/307/795/GCF_000307795.1/GCF_000307795.1.chrom.sizes.txt"
    }
  },
  "refNameAliases": {
    "adapter": {
      "type": "RefNameAliasAdapter",
      "refNameColumnHeaderName": "ucsc",
      "uri": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/307/795/GCF_000307795.1/GCF_000307795.1.chromAlias.txt"
    }
  }
}

refNameColumnHeaderName makes the UCSC name canonical, so the views read NC_018939v1 where the FASTA and the PAF say NC_018939.1, and the alias table maps one to the other. The alignment then goes on under the hub names:

jbrowse add-track 26695_vs_j99.paf -a GCF_000307795.1,GCF_000982695.1 --load copy

The -a order is query,target, the reverse of the minimap2 argument order: minimap2 target.fa query.fa becomes add-track -a query,target.

Reading the whole genome in a dotplot

Add → Dotplot view opens the import form in Quick start: pick the track just added and click Launch. Swap? transposes the axes. Manual picks each axis and a synteny file by hand.

The dotplot import form in Manual mode, where you pick the X-axis and Y-axis assembly by hand, then optionally add a synteny file in any of the formats it accepts. 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%2Fhpylori%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22DotplotView%22%2C%22views%22%3A%5B%7B%7D%2C%7B%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+sv_synteny%2Fdotplot_import

With your own data, the steps behind the figure:

  1. Open the view: Add → Dotplot view, and choose both axes in the import form.

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 the view: Add → Dotplot view, and choose both axes in the import form.

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

{
  "views": [
    {
      "type": "DotplotView",
      "views": [
        {},
        {}
      ]
    }
  ]
}

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/hpylori/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "DotplotView",
            "views": [
                {},
                {}
            ]
        }
    ],
)
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",
      "views": [
        {},
        {}
      ]
    }
  ]
}
JSON

npx @jbrowse/img dotplot --config https://jbrowse.org/demos/hpylori/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": "DotplotView",
      "views": [
        {},
        {}
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/hpylori/config.json \
  --width 1500 --height 561 \
  --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 26695 vs J99 alignment, 26695 on the X-axis and J99 on the Y-axis. The backbone runs anti-diagonal because the two assemblies were deposited in opposite orientations, and the pieces sitting off it are the rearrangements between the strains. 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%2Fhpylori%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22DotplotView%22%2C%22tracks%22%3A%5B%2226695_vs_j99.pif%22%5D%2C%22views%22%3A%5B%7B%22assembly%22%3A%22GCF_000307795.1%22%7D%2C%7B%22assembly%22%3A%22GCF_000982695.1%22%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+sv_synteny%2Fdotplot

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 GCF_000307795.1 on X and GCF_000982695.1 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. This one needs a bgzip-indexed PAF (.pif.gz + .tbi).A synteny track the session already has is quicker: pick it under Quick start, which fills in both axes itself.This figure uses “26695_vs_j99.pif”.
  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 GCF_000307795.1 on X and GCF_000982695.1 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. This one needs a bgzip-indexed PAF (.pif.gz + .tbi).A synteny track the session already has is quicker: pick it under Quick start, which fills in both axes itself.This figure uses “26695_vs_j99.pif”.
  4. Click Launch.

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

{
  "views": [
    {
      "type": "DotplotView",
      "tracks": [
        "26695_vs_j99.pif"
      ],
      "views": [
        {
          "assembly": "GCF_000307795.1"
        },
        {
          "assembly": "GCF_000982695.1"
        }
      ]
    }
  ]
}

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/hpylori/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "DotplotView",
            "tracks": [
                "26695_vs_j99.pif"
            ],
            "views": [
                {
                    "assembly": "GCF_000307795.1"
                },
                {
                    "assembly": "GCF_000982695.1"
                }
            ]
        }
    ],
)
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": [
        "26695_vs_j99.pif"
      ],
      "views": [
        {
          "assembly": "GCF_000307795.1"
        },
        {
          "assembly": "GCF_000982695.1"
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/img dotplot --config https://jbrowse.org/demos/hpylori/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": "DotplotView",
      "tracks": [
        "26695_vs_j99.pif"
      ],
      "views": [
        {
          "assembly": "GCF_000307795.1"
        },
        {
          "assembly": "GCF_000982695.1"
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/hpylori/config.json \
  --width 1500 --height 800 \
  --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.

To open any of those pieces at base resolution, drag a box across it, then right-click inside the box and choose Linear synteny view.

Stacking the three strains

A band is drawn between adjacent rows only, so a 26695 / CHC155 / J99 stack needs the two adjacent alignments:

minimap2 -c -x asm20 --eqx hpylori_chc155.fa.gz hpylori_26695.fa.gz > 26695_vs_chc155.paf
minimap2 -c -x asm20 --eqx hpylori_j99.fa.gz hpylori_chc155.fa.gz > chc155_vs_j99.paf

Take the third assembly from its hub and add both alignments the same way as above, then:

  1. Add → Linear synteny view, then switch to Manual.
  2. Pick an assembly per row, with Add row for the third.
  3. Click the arrow between each adjacent pair to choose that band's synteny track: 26695 against CHC155, then CHC155 against J99.
  4. Click Launch, and all three strains stack in one view.

A whole strain has about as many genes as its row has pixels, so zoom each row in once with its magnifier, then open each strain's gene track, NCBI RefSeq - RefSeq All (GFF), from its own track selector.

The four steps above and the gene tracks after them: Manual, a genome per row with Add row for the third, each connector showing the alignment it resolved for that pair, Launch, a zoom in on each row, and each strain's gene track from the track selector for that row. Open the session this video starts in ↗

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

  1. Choose Manual, then set a genome for each row
  2. Add a third row for the third strain
  3. Each arrow between rows has already found its alignment
  4. It opens empty; add each strain's genes from its own row
  5. Three strains stacked with their genes, alignments drawn between

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%2Fhpylori%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearSyntenyView%22%2C%22views%22%3A%5B%7B%7D%2C%7B%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+synteny%2Fthree_strain_import

With your own data, the steps behind the figure:

  1. Open the view: Add → Linear synteny view, and choose the rows in the import form.

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 the view: Add → Linear synteny view, and choose the rows in the import form.

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

{
  "views": [
    {
      "type": "LinearSyntenyView",
      "views": [
        {},
        {}
      ]
    }
  ]
}

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/hpylori/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearSyntenyView",
            "views": [
                {},
                {}
            ]
        }
    ],
)
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": [
        {},
        {}
      ]
    }
  ]
}
JSON

npx @jbrowse/img synteny --config https://jbrowse.org/demos/hpylori/config.json \
  --spec session.json \
  --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": "LinearSyntenyView",
      "views": [
        {},
        {}
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/hpylori/config.json \
  --width 1920 --height 960 \
  --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.

Three H. pylori strains stacked with a gene track on each genome. Ribbons connect aligned blocks between adjacent genomes, and genes such as prfB, fliR, cbf2 and efp line up across all three strains. 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%2Fhpylori%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearSyntenyView%22%2C%22drawCurves%22%3Atrue%2C%22tracks%22%3A%5B%5B%2226695_vs_chc155.pif%22%5D%2C%5B%22chc155_vs_j99.pif%22%5D%5D%2C%22views%22%3A%5B%7B%22loc%22%3A%22NC_018939v1%3A177696-190329%22%2C%22assembly%22%3A%22GCF_000307795.1%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22GCF_000307795.1-ncbiGff%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22showOnlyGenes%22%3Atrue%7D%5D%7D%2C%7B%22loc%22%3A%22NZ_AP026446v1%3A287157-299790%22%2C%22assembly%22%3A%22GCF_025998455.1%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22GCF_025998455.1-ncbiGff%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22showOnlyGenes%22%3Atrue%7D%5D%7D%2C%7B%22loc%22%3A%22NZ_CP011330v1%3A872350-884982%5Brev%5D%22%2C%22assembly%22%3A%22GCF_000982695.1%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22GCF_000982695.1-ncbiGff%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22showOnlyGenes%22%3Atrue%7D%5D%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+sv_synteny%2Flinear_synteny_genes

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: GCF_000307795.1, GCF_025998455.1, GCF_000982695.1.
  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. This one needs a bgzip-indexed PAF (.pif.gz + .tbi).A synteny track the session already has is quicker: pick it under Quick start, which fills in the rows itself.This figure uses “26695_vs_chc155.pif”.
  4. 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. This one needs a bgzip-indexed PAF (.pif.gz + .tbi).This figure uses “chc155_vs_j99.pif”.
  5. Click Launch.
  6. Synteny display settings (the sliders button in the view header) → Curved lines (checked)
  7. Row 1 (GCF_000307795.1)
    1. 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 “NCBI RefSeq - RefSeq All (GFF)”.
      1. Track menu → Show only genes (checked)
    2. Type your region of interest into the location box and press Enter.This figure is at NC_018939v1:177696-190329.
  8. Row 2 (GCF_025998455.1)
    1. 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 “NCBI RefSeq - RefSeq All (GFF)”.
      1. Track menu → Show only genes (checked)
    2. Type your region of interest into the location box and press Enter.This figure is at NZ_AP026446v1:287157-299790.
  9. Row 3 (GCF_000982695.1)
    1. 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 “NCBI RefSeq - RefSeq All (GFF)”.
      1. Track menu → Show only genes (checked)
    2. Type your region of interest into the location box and press Enter.This figure is at NZ_CP011330v1:872350-884982[rev].

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: GCF_000307795.1, GCF_025998455.1, GCF_000982695.1.
  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. This one needs a bgzip-indexed PAF (.pif.gz + .tbi).A synteny track the session already has is quicker: pick it under Quick start, which fills in the rows itself.This figure uses “26695_vs_chc155.pif”.
  4. 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. This one needs a bgzip-indexed PAF (.pif.gz + .tbi).This figure uses “chc155_vs_j99.pif”.
  5. Click Launch.
  6. Synteny display settings (the sliders button in the view header) → Curved lines (checked)
  7. Row 1 (GCF_000307795.1)
    1. 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 “NCBI RefSeq - RefSeq All (GFF)”.
      1. Track menu → Show only genes (checked)
    2. Type your region of interest into the location box and press Enter.This figure is at NC_018939v1:177696-190329.
  8. Row 2 (GCF_025998455.1)
    1. 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 “NCBI RefSeq - RefSeq All (GFF)”.
      1. Track menu → Show only genes (checked)
    2. Type your region of interest into the location box and press Enter.This figure is at NZ_AP026446v1:287157-299790.
  9. Row 3 (GCF_000982695.1)
    1. 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 “NCBI RefSeq - RefSeq All (GFF)”.
      1. Track menu → Show only genes (checked)
    2. Type your region of interest into the location box and press Enter.This figure is at NZ_CP011330v1:872350-884982[rev].

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

{
  "views": [
    {
      "type": "LinearSyntenyView",
      "drawCurves": true,
      "tracks": [
        [
          "26695_vs_chc155.pif"
        ],
        [
          "chc155_vs_j99.pif"
        ]
      ],
      "views": [
        {
          "loc": "NC_018939v1:177696-190329",
          "assembly": "GCF_000307795.1",
          "tracks": [
            {
              "trackId": "GCF_000307795.1-ncbiGff",
              "type": "LinearBasicDisplay",
              "showOnlyGenes": true
            }
          ]
        },
        {
          "loc": "NZ_AP026446v1:287157-299790",
          "assembly": "GCF_025998455.1",
          "tracks": [
            {
              "trackId": "GCF_025998455.1-ncbiGff",
              "type": "LinearBasicDisplay",
              "showOnlyGenes": true
            }
          ]
        },
        {
          "loc": "NZ_CP011330v1:872350-884982[rev]",
          "assembly": "GCF_000982695.1",
          "tracks": [
            {
              "trackId": "GCF_000982695.1-ncbiGff",
              "type": "LinearBasicDisplay",
              "showOnlyGenes": 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/hpylori/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearSyntenyView",
            "drawCurves": True,
            "tracks": [
                [
                    "26695_vs_chc155.pif"
                ],
                [
                    "chc155_vs_j99.pif"
                ]
            ],
            "views": [
                {
                    "loc": "NC_018939v1:177696-190329",
                    "assembly": "GCF_000307795.1",
                    "tracks": [
                        {
                            "trackId": "GCF_000307795.1-ncbiGff",
                            "type": "LinearBasicDisplay",
                            "showOnlyGenes": True
                        }
                    ]
                },
                {
                    "loc": "NZ_AP026446v1:287157-299790",
                    "assembly": "GCF_025998455.1",
                    "tracks": [
                        {
                            "trackId": "GCF_025998455.1-ncbiGff",
                            "type": "LinearBasicDisplay",
                            "showOnlyGenes": True
                        }
                    ]
                },
                {
                    "loc": "NZ_CP011330v1:872350-884982[rev]",
                    "assembly": "GCF_000982695.1",
                    "tracks": [
                        {
                            "trackId": "GCF_000982695.1-ncbiGff",
                            "type": "LinearBasicDisplay",
                            "showOnlyGenes": 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",
      "drawCurves": true,
      "tracks": [
        [
          "26695_vs_chc155.pif"
        ],
        [
          "chc155_vs_j99.pif"
        ]
      ],
      "views": [
        {
          "loc": "NC_018939v1:177696-190329",
          "assembly": "GCF_000307795.1",
          "tracks": [
            {
              "trackId": "GCF_000307795.1-ncbiGff",
              "type": "LinearBasicDisplay",
              "showOnlyGenes": true
            }
          ]
        },
        {
          "loc": "NZ_AP026446v1:287157-299790",
          "assembly": "GCF_025998455.1",
          "tracks": [
            {
              "trackId": "GCF_025998455.1-ncbiGff",
              "type": "LinearBasicDisplay",
              "showOnlyGenes": true
            }
          ]
        },
        {
          "loc": "NZ_CP011330v1:872350-884982[rev]",
          "assembly": "GCF_000982695.1",
          "tracks": [
            {
              "trackId": "GCF_000982695.1-ncbiGff",
              "type": "LinearBasicDisplay",
              "showOnlyGenes": true
            }
          ]
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/img synteny --config https://jbrowse.org/demos/hpylori/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",
      "drawCurves": true,
      "tracks": [
        [
          "26695_vs_chc155.pif"
        ],
        [
          "chc155_vs_j99.pif"
        ]
      ],
      "views": [
        {
          "loc": "NC_018939v1:177696-190329",
          "assembly": "GCF_000307795.1",
          "tracks": [
            {
              "trackId": "GCF_000307795.1-ncbiGff",
              "type": "LinearBasicDisplay",
              "showOnlyGenes": true
            }
          ]
        },
        {
          "loc": "NZ_AP026446v1:287157-299790",
          "assembly": "GCF_025998455.1",
          "tracks": [
            {
              "trackId": "GCF_025998455.1-ncbiGff",
              "type": "LinearBasicDisplay",
              "showOnlyGenes": true
            }
          ]
        },
        {
          "loc": "NZ_CP011330v1:872350-884982[rev]",
          "assembly": "GCF_000982695.1",
          "tracks": [
            {
              "trackId": "GCF_000982695.1-ncbiGff",
              "type": "LinearBasicDisplay",
              "showOnlyGenes": true
            }
          ]
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/hpylori/config.json \
  --width 1500 --height 822 \
  --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.

Each panel is a full linear genome view with its own search box, zoom and track selector. See Linear synteny view for ribbon options and URL parameters → linear synteny view for building one from a URL.

Coloring genes by ortholog

In bacteria the gene symbol is effectively the ortholog id, since NCBI reuses standardized symbols across strains. On each gene track, pick Color by... → Attribute... from the track menu and enter gene. Every distinct value gets its own color from one palette, chosen from the value itself, so an ortholog carries one color down all three panels. Features with no value are grey; most genes here carry only a locus tag.

The click and its result. Left, the Color by attribute dialog on the first strain's gene track with the attribute name set to gene. Right, the same three strains after applying it: a shared symbol holds one color down all three panels. Open in JBrowse: Dialog ↗ · Result ↗

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%2Fhpylori%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearSyntenyView%22%2C%22drawCurves%22%3Atrue%2C%22tracks%22%3A%5B%5B%2226695_vs_chc155.pif%22%5D%2C%5B%22chc155_vs_j99.pif%22%5D%5D%2C%22views%22%3A%5B%7B%22loc%22%3A%22NC_018939v1%3A177696-190329%22%2C%22assembly%22%3A%22GCF_000307795.1%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22GCF_000307795.1-ncbiGff%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22showOnlyGenes%22%3Atrue%7D%5D%7D%2C%7B%22loc%22%3A%22NZ_AP026446v1%3A287157-299790%22%2C%22assembly%22%3A%22GCF_025998455.1%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22GCF_025998455.1-ncbiGff%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22showOnlyGenes%22%3Atrue%7D%5D%7D%2C%7B%22loc%22%3A%22NZ_CP011330v1%3A872350-884982%5Brev%5D%22%2C%22assembly%22%3A%22GCF_000982695.1%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22GCF_000982695.1-ncbiGff%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22showOnlyGenes%22%3Atrue%7D%5D%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+sv_synteny%2Fcolor_by_attribute

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: GCF_000307795.1, GCF_025998455.1, GCF_000982695.1.
  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. This one needs a bgzip-indexed PAF (.pif.gz + .tbi).A synteny track the session already has is quicker: pick it under Quick start, which fills in the rows itself.This figure uses “26695_vs_chc155.pif”.
  4. 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. This one needs a bgzip-indexed PAF (.pif.gz + .tbi).This figure uses “chc155_vs_j99.pif”.
  5. Click Launch.
  6. Synteny display settings (the sliders button in the view header) → Curved lines (checked)
  7. Row 1 (GCF_000307795.1)
    1. 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 “NCBI RefSeq - RefSeq All (GFF)”.
      1. Track menu → Show only genes (checked)
    2. Type your region of interest into the location box and press Enter.This figure is at NC_018939v1:177696-190329.
  8. Row 2 (GCF_025998455.1)
    1. 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 “NCBI RefSeq - RefSeq All (GFF)”.
      1. Track menu → Show only genes (checked)
    2. Type your region of interest into the location box and press Enter.This figure is at NZ_AP026446v1:287157-299790.
  9. Row 3 (GCF_000982695.1)
    1. 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 “NCBI RefSeq - RefSeq All (GFF)”.
      1. Track menu → Show only genes (checked)
    2. Type your region of interest into the location box and press Enter.This figure is at NZ_CP011330v1:872350-884982[rev].

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: GCF_000307795.1, GCF_025998455.1, GCF_000982695.1.
  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. This one needs a bgzip-indexed PAF (.pif.gz + .tbi).A synteny track the session already has is quicker: pick it under Quick start, which fills in the rows itself.This figure uses “26695_vs_chc155.pif”.
  4. 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. This one needs a bgzip-indexed PAF (.pif.gz + .tbi).This figure uses “chc155_vs_j99.pif”.
  5. Click Launch.
  6. Synteny display settings (the sliders button in the view header) → Curved lines (checked)
  7. Row 1 (GCF_000307795.1)
    1. 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 “NCBI RefSeq - RefSeq All (GFF)”.
      1. Track menu → Show only genes (checked)
    2. Type your region of interest into the location box and press Enter.This figure is at NC_018939v1:177696-190329.
  8. Row 2 (GCF_025998455.1)
    1. 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 “NCBI RefSeq - RefSeq All (GFF)”.
      1. Track menu → Show only genes (checked)
    2. Type your region of interest into the location box and press Enter.This figure is at NZ_AP026446v1:287157-299790.
  9. Row 3 (GCF_000982695.1)
    1. 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 “NCBI RefSeq - RefSeq All (GFF)”.
      1. Track menu → Show only genes (checked)
    2. Type your region of interest into the location box and press Enter.This figure is at NZ_CP011330v1:872350-884982[rev].

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

{
  "views": [
    {
      "type": "LinearSyntenyView",
      "drawCurves": true,
      "tracks": [
        [
          "26695_vs_chc155.pif"
        ],
        [
          "chc155_vs_j99.pif"
        ]
      ],
      "views": [
        {
          "loc": "NC_018939v1:177696-190329",
          "assembly": "GCF_000307795.1",
          "tracks": [
            {
              "trackId": "GCF_000307795.1-ncbiGff",
              "type": "LinearBasicDisplay",
              "showOnlyGenes": true
            }
          ]
        },
        {
          "loc": "NZ_AP026446v1:287157-299790",
          "assembly": "GCF_025998455.1",
          "tracks": [
            {
              "trackId": "GCF_025998455.1-ncbiGff",
              "type": "LinearBasicDisplay",
              "showOnlyGenes": true
            }
          ]
        },
        {
          "loc": "NZ_CP011330v1:872350-884982[rev]",
          "assembly": "GCF_000982695.1",
          "tracks": [
            {
              "trackId": "GCF_000982695.1-ncbiGff",
              "type": "LinearBasicDisplay",
              "showOnlyGenes": 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/hpylori/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearSyntenyView",
            "drawCurves": True,
            "tracks": [
                [
                    "26695_vs_chc155.pif"
                ],
                [
                    "chc155_vs_j99.pif"
                ]
            ],
            "views": [
                {
                    "loc": "NC_018939v1:177696-190329",
                    "assembly": "GCF_000307795.1",
                    "tracks": [
                        {
                            "trackId": "GCF_000307795.1-ncbiGff",
                            "type": "LinearBasicDisplay",
                            "showOnlyGenes": True
                        }
                    ]
                },
                {
                    "loc": "NZ_AP026446v1:287157-299790",
                    "assembly": "GCF_025998455.1",
                    "tracks": [
                        {
                            "trackId": "GCF_025998455.1-ncbiGff",
                            "type": "LinearBasicDisplay",
                            "showOnlyGenes": True
                        }
                    ]
                },
                {
                    "loc": "NZ_CP011330v1:872350-884982[rev]",
                    "assembly": "GCF_000982695.1",
                    "tracks": [
                        {
                            "trackId": "GCF_000982695.1-ncbiGff",
                            "type": "LinearBasicDisplay",
                            "showOnlyGenes": 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",
      "drawCurves": true,
      "tracks": [
        [
          "26695_vs_chc155.pif"
        ],
        [
          "chc155_vs_j99.pif"
        ]
      ],
      "views": [
        {
          "loc": "NC_018939v1:177696-190329",
          "assembly": "GCF_000307795.1",
          "tracks": [
            {
              "trackId": "GCF_000307795.1-ncbiGff",
              "type": "LinearBasicDisplay",
              "showOnlyGenes": true
            }
          ]
        },
        {
          "loc": "NZ_AP026446v1:287157-299790",
          "assembly": "GCF_025998455.1",
          "tracks": [
            {
              "trackId": "GCF_025998455.1-ncbiGff",
              "type": "LinearBasicDisplay",
              "showOnlyGenes": true
            }
          ]
        },
        {
          "loc": "NZ_CP011330v1:872350-884982[rev]",
          "assembly": "GCF_000982695.1",
          "tracks": [
            {
              "trackId": "GCF_000982695.1-ncbiGff",
              "type": "LinearBasicDisplay",
              "showOnlyGenes": true
            }
          ]
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/img synteny --config https://jbrowse.org/demos/hpylori/config.json \
  --spec session.json \
  --width 900 --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",
      "drawCurves": true,
      "tracks": [
        [
          "26695_vs_chc155.pif"
        ],
        [
          "chc155_vs_j99.pif"
        ]
      ],
      "views": [
        {
          "loc": "NC_018939v1:177696-190329",
          "assembly": "GCF_000307795.1",
          "tracks": [
            {
              "trackId": "GCF_000307795.1-ncbiGff",
              "type": "LinearBasicDisplay",
              "showOnlyGenes": true
            }
          ]
        },
        {
          "loc": "NZ_AP026446v1:287157-299790",
          "assembly": "GCF_025998455.1",
          "tracks": [
            {
              "trackId": "GCF_025998455.1-ncbiGff",
              "type": "LinearBasicDisplay",
              "showOnlyGenes": true
            }
          ]
        },
        {
          "loc": "NZ_CP011330v1:872350-884982[rev]",
          "assembly": "GCF_000982695.1",
          "tracks": [
            {
              "trackId": "GCF_000982695.1-ncbiGff",
              "type": "LinearBasicDisplay",
              "showOnlyGenes": true
            }
          ]
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/hpylori/config.json \
  --width 900 --height 842 \
  --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%2Fhpylori%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearSyntenyView%22%2C%22drawCurves%22%3Atrue%2C%22tracks%22%3A%5B%5B%2226695_vs_chc155.pif%22%5D%2C%5B%22chc155_vs_j99.pif%22%5D%5D%2C%22views%22%3A%5B%7B%22loc%22%3A%22NC_018939v1%3A177696-190329%22%2C%22assembly%22%3A%22GCF_000307795.1%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22GCF_000307795.1-ncbiGff%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22showOnlyGenes%22%3Atrue%2C%22color%22%3A%7B%22field%22%3A%22gene%22%7D%2C%22showLegend%22%3Afalse%7D%5D%7D%2C%7B%22loc%22%3A%22NZ_AP026446v1%3A287157-299790%22%2C%22assembly%22%3A%22GCF_025998455.1%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22GCF_025998455.1-ncbiGff%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22showOnlyGenes%22%3Atrue%2C%22color%22%3A%7B%22field%22%3A%22gene%22%7D%2C%22showLegend%22%3Afalse%7D%5D%7D%2C%7B%22loc%22%3A%22NZ_CP011330v1%3A872350-884982%5Brev%5D%22%2C%22assembly%22%3A%22GCF_000982695.1%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22GCF_000982695.1-ncbiGff%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22showOnlyGenes%22%3Atrue%2C%22color%22%3A%7B%22field%22%3A%22gene%22%7D%2C%22showLegend%22%3Afalse%7D%5D%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+sv_synteny%2Fortholog_colors

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: GCF_000307795.1, GCF_025998455.1, GCF_000982695.1.
  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. This one needs a bgzip-indexed PAF (.pif.gz + .tbi).A synteny track the session already has is quicker: pick it under Quick start, which fills in the rows itself.This figure uses “26695_vs_chc155.pif”.
  4. 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. This one needs a bgzip-indexed PAF (.pif.gz + .tbi).This figure uses “chc155_vs_j99.pif”.
  5. Click Launch.
  6. Synteny display settings (the sliders button in the view header) → Curved lines (checked)
  7. Row 1 (GCF_000307795.1)
    1. 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 “NCBI RefSeq - RefSeq All (GFF)”.
      1. Track menu → Show only genes (checked)
      2. Track menu → Color by... → Attribute... → gene
    2. Type your region of interest into the location box and press Enter.This figure is at NC_018939v1:177696-190329.
  8. Row 2 (GCF_025998455.1)
    1. 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 “NCBI RefSeq - RefSeq All (GFF)”.
      1. Track menu → Show only genes (checked)
      2. Track menu → Color by... → Attribute... → gene
    2. Type your region of interest into the location box and press Enter.This figure is at NZ_AP026446v1:287157-299790.
  9. Row 3 (GCF_000982695.1)
    1. 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 “NCBI RefSeq - RefSeq All (GFF)”.
      1. Track menu → Show only genes (checked)
      2. Track menu → Color by... → Attribute... → gene
    2. Type your region of interest into the location box and press Enter.This figure is at NZ_CP011330v1:872350-884982[rev].

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 genomes in your JBrowse Web's config.json: run jbrowse add-assembly once for each.This figure's rows, top to bottom: GCF_000307795.1, GCF_025998455.1, GCF_000982695.1.
  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. This one needs a bgzip-indexed PAF (.pif.gz + .tbi).A synteny track the session already has is quicker: pick it under Quick start, which fills in the rows itself.This figure uses “26695_vs_chc155.pif”.
  4. 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. This one needs a bgzip-indexed PAF (.pif.gz + .tbi).This figure uses “chc155_vs_j99.pif”.
  5. Click Launch.
  6. Synteny display settings (the sliders button in the view header) → Curved lines (checked)
  7. Row 1 (GCF_000307795.1)
    1. 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 “NCBI RefSeq - RefSeq All (GFF)”.
      1. Track menu → Show only genes (checked)
      2. Track menu → Color by... → Attribute... → gene
    2. Type your region of interest into the location box and press Enter.This figure is at NC_018939v1:177696-190329.
  8. Row 2 (GCF_025998455.1)
    1. 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 “NCBI RefSeq - RefSeq All (GFF)”.
      1. Track menu → Show only genes (checked)
      2. Track menu → Color by... → Attribute... → gene
    2. Type your region of interest into the location box and press Enter.This figure is at NZ_AP026446v1:287157-299790.
  9. Row 3 (GCF_000982695.1)
    1. 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 “NCBI RefSeq - RefSeq All (GFF)”.
      1. Track menu → Show only genes (checked)
      2. Track menu → Color by... → Attribute... → gene
    2. Type your region of interest into the location box and press Enter.This figure is at NZ_CP011330v1:872350-884982[rev].

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

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

{
  "views": [
    {
      "type": "LinearSyntenyView",
      "drawCurves": true,
      "tracks": [
        [
          "26695_vs_chc155.pif"
        ],
        [
          "chc155_vs_j99.pif"
        ]
      ],
      "views": [
        {
          "loc": "NC_018939v1:177696-190329",
          "assembly": "GCF_000307795.1",
          "tracks": [
            {
              "trackId": "GCF_000307795.1-ncbiGff",
              "type": "LinearBasicDisplay",
              "showOnlyGenes": true,
              "color": {
                "field": "gene"
              },
              "showLegend": false
            }
          ]
        },
        {
          "loc": "NZ_AP026446v1:287157-299790",
          "assembly": "GCF_025998455.1",
          "tracks": [
            {
              "trackId": "GCF_025998455.1-ncbiGff",
              "type": "LinearBasicDisplay",
              "showOnlyGenes": true,
              "color": {
                "field": "gene"
              },
              "showLegend": false
            }
          ]
        },
        {
          "loc": "NZ_CP011330v1:872350-884982[rev]",
          "assembly": "GCF_000982695.1",
          "tracks": [
            {
              "trackId": "GCF_000982695.1-ncbiGff",
              "type": "LinearBasicDisplay",
              "showOnlyGenes": true,
              "color": {
                "field": "gene"
              },
              "showLegend": false
            }
          ]
        }
      ]
    }
  ]
}

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/hpylori/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearSyntenyView",
            "drawCurves": True,
            "tracks": [
                [
                    "26695_vs_chc155.pif"
                ],
                [
                    "chc155_vs_j99.pif"
                ]
            ],
            "views": [
                {
                    "loc": "NC_018939v1:177696-190329",
                    "assembly": "GCF_000307795.1",
                    "tracks": [
                        {
                            "trackId": "GCF_000307795.1-ncbiGff",
                            "type": "LinearBasicDisplay",
                            "showOnlyGenes": True,
                            "color": {
                                "field": "gene"
                            },
                            "showLegend": False
                        }
                    ]
                },
                {
                    "loc": "NZ_AP026446v1:287157-299790",
                    "assembly": "GCF_025998455.1",
                    "tracks": [
                        {
                            "trackId": "GCF_025998455.1-ncbiGff",
                            "type": "LinearBasicDisplay",
                            "showOnlyGenes": True,
                            "color": {
                                "field": "gene"
                            },
                            "showLegend": False
                        }
                    ]
                },
                {
                    "loc": "NZ_CP011330v1:872350-884982[rev]",
                    "assembly": "GCF_000982695.1",
                    "tracks": [
                        {
                            "trackId": "GCF_000982695.1-ncbiGff",
                            "type": "LinearBasicDisplay",
                            "showOnlyGenes": True,
                            "color": {
                                "field": "gene"
                            },
                            "showLegend": False
                        }
                    ]
                }
            ]
        }
    ],
)
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",
      "drawCurves": true,
      "tracks": [
        [
          "26695_vs_chc155.pif"
        ],
        [
          "chc155_vs_j99.pif"
        ]
      ],
      "views": [
        {
          "loc": "NC_018939v1:177696-190329",
          "assembly": "GCF_000307795.1",
          "tracks": [
            {
              "trackId": "GCF_000307795.1-ncbiGff",
              "type": "LinearBasicDisplay",
              "showOnlyGenes": true,
              "color": {
                "field": "gene"
              },
              "showLegend": false
            }
          ]
        },
        {
          "loc": "NZ_AP026446v1:287157-299790",
          "assembly": "GCF_025998455.1",
          "tracks": [
            {
              "trackId": "GCF_025998455.1-ncbiGff",
              "type": "LinearBasicDisplay",
              "showOnlyGenes": true,
              "color": {
                "field": "gene"
              },
              "showLegend": false
            }
          ]
        },
        {
          "loc": "NZ_CP011330v1:872350-884982[rev]",
          "assembly": "GCF_000982695.1",
          "tracks": [
            {
              "trackId": "GCF_000982695.1-ncbiGff",
              "type": "LinearBasicDisplay",
              "showOnlyGenes": true,
              "color": {
                "field": "gene"
              },
              "showLegend": false
            }
          ]
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/img synteny --config https://jbrowse.org/demos/hpylori/config.json \
  --spec session.json \
  --width 900 --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",
      "drawCurves": true,
      "tracks": [
        [
          "26695_vs_chc155.pif"
        ],
        [
          "chc155_vs_j99.pif"
        ]
      ],
      "views": [
        {
          "loc": "NC_018939v1:177696-190329",
          "assembly": "GCF_000307795.1",
          "tracks": [
            {
              "trackId": "GCF_000307795.1-ncbiGff",
              "type": "LinearBasicDisplay",
              "showOnlyGenes": true,
              "color": {
                "field": "gene"
              },
              "showLegend": false
            }
          ]
        },
        {
          "loc": "NZ_AP026446v1:287157-299790",
          "assembly": "GCF_025998455.1",
          "tracks": [
            {
              "trackId": "GCF_025998455.1-ncbiGff",
              "type": "LinearBasicDisplay",
              "showOnlyGenes": true,
              "color": {
                "field": "gene"
              },
              "showLegend": false
            }
          ]
        },
        {
          "loc": "NZ_CP011330v1:872350-884982[rev]",
          "assembly": "GCF_000982695.1",
          "tracks": [
            {
              "trackId": "GCF_000982695.1-ncbiGff",
              "type": "LinearBasicDisplay",
              "showOnlyGenes": true,
              "color": {
                "field": "gene"
              },
              "showLegend": false
            }
          ]
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/hpylori/config.json \
  --width 900 --height 842 \
  --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 dialog writes the field into the display's color, one line of config on the hub's gene track:

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

{
  "type": "FeatureTrack",
  "trackId": "GCF_000307795.1-ncbiGff",
  "name": "NCBI RefSeq - RefSeq All (GFF)",
  "assemblyNames": ["GCF_000307795.1"],
  "adapter": {
    "type": "Gff3TabixAdapter",
    "uri": "https://jbrowse.org/hubs/genark/GCF/000/307/795/GCF_000307795.1/GCF_000307795.1_ASM30779v1_genomic.gff.gz",
    "index": {
      "location": {
        "uri": "https://jbrowse.org/hubs/genark/GCF/000/307/795/GCF_000307795.1/GCF_000307795.1_ASM30779v1_genomic.gff.gz.csi"
      },
      "indexType": "CSI"
    }
  },
  "displayDefaults": {
    "showOnlyGenes": true,
    "color": { "field": "gene" }
  }
}
jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "GCF_000307795.1-ncbiGff",
  "name": "NCBI RefSeq - RefSeq All (GFF)",
  "assemblyNames": ["GCF_000307795.1"],
  "adapter": {
    "type": "Gff3TabixAdapter",
    "uri": "https://jbrowse.org/hubs/genark/GCF/000/307/795/GCF_000307795.1/GCF_000307795.1_ASM30779v1_genomic.gff.gz",
    "index": {
      "location": {
        "uri": "https://jbrowse.org/hubs/genark/GCF/000/307/795/GCF_000307795.1/GCF_000307795.1_ASM30779v1_genomic.gff.gz.csi"
      },
      "indexType": "CSI"
    }
  },
  "displayDefaults": {
    "showOnlyGenes": true,
    "color": { "field": "gene" }
  }
}'

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": "GCF_000307795.1-ncbiGff",
  "name": "NCBI RefSeq - RefSeq All (GFF)",
  "assemblyNames": ["GCF_000307795.1"],
  "adapter": {
    "type": "Gff3TabixAdapter",
    "uri": "https://jbrowse.org/hubs/genark/GCF/000/307/795/GCF_000307795.1/GCF_000307795.1_ASM30779v1_genomic.gff.gz",
    "index": {
      "location": {
        "uri": "https://jbrowse.org/hubs/genark/GCF/000/307/795/GCF_000307795.1/GCF_000307795.1_ASM30779v1_genomic.gff.gz.csi"
      },
      "indexType": "CSI"
    }
  },
  "displayDefaults": {
    "showOnlyGenes": true,
    "color": { "field": "gene" }
  }
}

Using PIF for large genomes

A bacterial PAF is small enough to load whole. For a large whole-genome alignment, convert it to PIF (Pairwise Indexed Format) so JBrowse fetches only the alignments in the current viewport:

jbrowse make-pif alignment.paf
jbrowse add-track alignment.pif.gz -a query,target --load copy

Troubleshooting

assemblyNames in the wrong order is the common one. JBrowse checks at view load whether the top row's chromosome names belong to that assembly, and a warning in the view header names the remedy when they belong to the other row.

A synteny track whose assemblyNames are reversed. No chromosome name resolves, so the band is empty, and the warning icon in the header opens a dialog reporting the reversal. 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%2Fhpylori%2Fconfig.json&session=spec-%7B%22sessionTracks%22%3A%5B%7B%22type%22%3A%22SyntenyTrack%22%2C%22trackId%22%3A%22hpylori_reversed_assembly_names%22%2C%22name%22%3A%2226695+vs+CHC155+%28assemblyNames+reversed%29%22%2C%22assemblyNames%22%3A%5B%22GCF_000307795.1%22%2C%22GCF_025998455.1%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22PairwiseIndexedPAFAdapter%22%2C%22assemblyNames%22%3A%5B%22GCF_000307795.1%22%2C%22GCF_025998455.1%22%5D%2C%22pifGzLocation%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fhpylori%2F26695_vs_chc155.pif.gz%22%2C%22locationType%22%3A%22UriLocation%22%7D%2C%22index%22%3A%7B%22indexType%22%3A%22TBI%22%2C%22location%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fhpylori%2F26695_vs_chc155.pif.gz.tbi%22%2C%22locationType%22%3A%22UriLocation%22%7D%7D%7D%7D%5D%2C%22views%22%3A%5B%7B%22type%22%3A%22LinearSyntenyView%22%2C%22tracks%22%3A%5B%5B%22hpylori_reversed_assembly_names%22%5D%5D%2C%22collapseEmptyRows%22%3Atrue%2C%22levelHeights%22%3A%5B200%5D%2C%22views%22%3A%5B%7B%22assembly%22%3A%22GCF_000307795.1%22%2C%22loc%22%3A%22NC_018939v1%22%7D%2C%7B%22assembly%22%3A%22GCF_025998455.1%22%2C%22loc%22%3A%22NZ_AP026446v1%22%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+sv_synteny%2Fassembly_order_warning

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: GCF_000307795.1, GCF_025998455.1.
  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. This one needs a bgzip-indexed PAF (.pif.gz + .tbi).A synteny track the session already has is quicker: pick it under Quick start, which fills in the rows itself.This figure uses “26695 vs CHC155 (assemblyNames reversed)”.
  4. Click Launch.
  5. Drag the bar below a synteny level to resize it.This figure's level is 200px tall.
  6. Row 1 (GCF_000307795.1)
    1. Type your region of interest into the location box and press Enter.This figure is at NC_018939v1.
  7. Row 2 (GCF_025998455.1)
    1. Type your region of interest into the location box and press Enter.This figure is at NZ_AP026446v1.

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: GCF_000307795.1, GCF_025998455.1.
  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. This one needs a bgzip-indexed PAF (.pif.gz + .tbi).A synteny track the session already has is quicker: pick it under Quick start, which fills in the rows itself.This figure uses “26695 vs CHC155 (assemblyNames reversed)”.
  4. Click Launch.
  5. Drag the bar below a synteny level to resize it.This figure's level is 200px tall.
  6. Row 1 (GCF_000307795.1)
    1. Type your region of interest into the location box and press Enter.This figure is at NC_018939v1.
  7. Row 2 (GCF_025998455.1)
    1. Type your region of interest into the location box and press Enter.This figure is at NZ_AP026446v1.

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": "SyntenyTrack",
  "trackId": "hpylori_reversed_assembly_names",
  "name": "26695 vs CHC155 (assemblyNames reversed)",
  "assemblyNames": [
    "GCF_000307795.1",
    "GCF_025998455.1"
  ],
  "adapter": {
    "type": "PairwiseIndexedPAFAdapter",
    "assemblyNames": [
      "GCF_000307795.1",
      "GCF_025998455.1"
    ],
    "pifGzLocation": {
      "uri": "https://jbrowse.org/demos/hpylori/26695_vs_chc155.pif.gz",
      "locationType": "UriLocation"
    },
    "index": {
      "indexType": "TBI",
      "location": {
        "uri": "https://jbrowse.org/demos/hpylori/26695_vs_chc155.pif.gz.tbi",
        "locationType": "UriLocation"
      }
    }
  }
}'

Run these where the config.json is, or add --out <dir>, and point each uri at your own file. The config needs GCF_000307795.1, GCF_025998455.1 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 https://jbrowse.org/demos/hpylori/config.json: paste it after &session=spec- on a JBrowse Web link that loads that config.

{
  "sessionTracks": [
    {
      "type": "SyntenyTrack",
      "trackId": "hpylori_reversed_assembly_names",
      "name": "26695 vs CHC155 (assemblyNames reversed)",
      "assemblyNames": [
        "GCF_000307795.1",
        "GCF_025998455.1"
      ],
      "adapter": {
        "type": "PairwiseIndexedPAFAdapter",
        "assemblyNames": [
          "GCF_000307795.1",
          "GCF_025998455.1"
        ],
        "pifGzLocation": {
          "uri": "https://jbrowse.org/demos/hpylori/26695_vs_chc155.pif.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "indexType": "TBI",
          "location": {
            "uri": "https://jbrowse.org/demos/hpylori/26695_vs_chc155.pif.gz.tbi",
            "locationType": "UriLocation"
          }
        }
      }
    }
  ],
  "views": [
    {
      "type": "LinearSyntenyView",
      "tracks": [
        [
          "hpylori_reversed_assembly_names"
        ]
      ],
      "collapseEmptyRows": true,
      "levelHeights": [
        200
      ],
      "views": [
        {
          "assembly": "GCF_000307795.1",
          "loc": "NC_018939v1"
        },
        {
          "assembly": "GCF_025998455.1",
          "loc": "NZ_AP026446v1"
        }
      ]
    }
  ]
}

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/hpylori/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []) + [
        {
            "type": "SyntenyTrack",
            "trackId": "hpylori_reversed_assembly_names",
            "name": "26695 vs CHC155 (assemblyNames reversed)",
            "assemblyNames": [
                "GCF_000307795.1",
                "GCF_025998455.1"
            ],
            "adapter": {
                "type": "PairwiseIndexedPAFAdapter",
                "assemblyNames": [
                    "GCF_000307795.1",
                    "GCF_025998455.1"
                ],
                "pifGzLocation": {
                    "uri": "https://jbrowse.org/demos/hpylori/26695_vs_chc155.pif.gz",
                    "locationType": "UriLocation"
                },
                "index": {
                    "indexType": "TBI",
                    "location": {
                        "uri": "https://jbrowse.org/demos/hpylori/26695_vs_chc155.pif.gz.tbi",
                        "locationType": "UriLocation"
                    }
                }
            }
        }
    ],
    views=[
        {
            "type": "LinearSyntenyView",
            "tracks": [
                [
                    "hpylori_reversed_assembly_names"
                ]
            ],
            "collapseEmptyRows": True,
            "levelHeights": [
                200
            ],
            "views": [
                {
                    "assembly": "GCF_000307795.1",
                    "loc": "NC_018939v1"
                },
                {
                    "assembly": "GCF_025998455.1",
                    "loc": "NZ_AP026446v1"
                }
            ]
        }
    ],
)
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": "SyntenyTrack",
    "trackId": "hpylori_reversed_assembly_names",
    "name": "26695 vs CHC155 (assemblyNames reversed)",
    "assemblyNames": [
      "GCF_000307795.1",
      "GCF_025998455.1"
    ],
    "adapter": {
      "type": "PairwiseIndexedPAFAdapter",
      "assemblyNames": [
        "GCF_000307795.1",
        "GCF_025998455.1"
      ],
      "pifGzLocation": {
        "uri": "https://jbrowse.org/demos/hpylori/26695_vs_chc155.pif.gz",
        "locationType": "UriLocation"
      },
      "index": {
        "indexType": "TBI",
        "location": {
          "uri": "https://jbrowse.org/demos/hpylori/26695_vs_chc155.pif.gz.tbi",
          "locationType": "UriLocation"
        }
      }
    }
  }
]
JSON

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearSyntenyView",
      "tracks": [
        [
          "hpylori_reversed_assembly_names"
        ]
      ],
      "collapseEmptyRows": true,
      "levelHeights": [
        200
      ],
      "views": [
        {
          "assembly": "GCF_000307795.1",
          "loc": "NC_018939v1"
        },
        {
          "assembly": "GCF_025998455.1",
          "loc": "NZ_AP026446v1"
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/img synteny --config https://jbrowse.org/demos/hpylori/config.json \
  --tracks tracks.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'
{
  "sessionTracks": [
    {
      "type": "SyntenyTrack",
      "trackId": "hpylori_reversed_assembly_names",
      "name": "26695 vs CHC155 (assemblyNames reversed)",
      "assemblyNames": [
        "GCF_000307795.1",
        "GCF_025998455.1"
      ],
      "adapter": {
        "type": "PairwiseIndexedPAFAdapter",
        "assemblyNames": [
          "GCF_000307795.1",
          "GCF_025998455.1"
        ],
        "pifGzLocation": {
          "uri": "https://jbrowse.org/demos/hpylori/26695_vs_chc155.pif.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "indexType": "TBI",
          "location": {
            "uri": "https://jbrowse.org/demos/hpylori/26695_vs_chc155.pif.gz.tbi",
            "locationType": "UriLocation"
          }
        }
      }
    }
  ],
  "views": [
    {
      "type": "LinearSyntenyView",
      "tracks": [
        [
          "hpylori_reversed_assembly_names"
        ]
      ],
      "collapseEmptyRows": true,
      "levelHeights": [
        200
      ],
      "views": [
        {
          "assembly": "GCF_000307795.1",
          "loc": "NC_018939v1"
        },
        {
          "assembly": "GCF_025998455.1",
          "loc": "NZ_AP026446v1"
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/hpylori/config.json \
  --width 1500 --height 425 \
  --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.

A view that scatters its blocks randomly comes from a preset too tight for the divergence, which leaves only short spurious anchors. Raise it, and check -c --eqx were passed.

Reproduce it end to end

One script builds everything above, build_hpylori_synteny.sh:

curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/build_hpylori_synteny.sh
bash build_hpylori_synteny.sh          # builds ./hpylori_synteny_build/jbrowse2
npx --yes serve hpylori_synteny_build/jbrowse2 # then open the printed URL

The script downloads each strain's hub sequence and config, aligns the strain pairs, and writes a config.json with the three hub assemblies and gene tracks, the pairwise synteny tracks, and a default session stacking all three. It needs the tools under Prerequisites.

See also

References