Pangenome (cattle)

Opening in Desktop needs JBrowse Desktop 5.0+, and saves the view as a reopenable session.

https://jbrowse.org/code/jb2/main/?config=test_data%2Fgraphgenomeview%2Fpangenome_nonhuman.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22id%22%3A%22bovine-chr23-lgv%22%2C%22assembly%22%3A%22bosTau9%22%2C%22loc%22%3A%22chr23%22%2C%22tracks%22%3A%5B%22bosTau9_ncbiRefSeq_ucsc%22%2C%22bovine_bubble_score%22%2C%7B%22trackId%22%3A%22bovine_minigraph_tier%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+pangenome%2Fbovine_whole_chromosome

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 bosTau9, loaded from a .2bit genome.
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 “NCBI RefSeq genes (bosTau9)”.
3. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “Bovine super-pangenome: variability (segments per bubble)”.
4. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “Bovine super-pangenome: bubble 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 (60px here).
5. Type your region of interest into the location box and press Enter.This figure is at chr23.

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 bosTau9, loaded from a .2bit genome.
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 “NCBI RefSeq genes (bosTau9)”.
3. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “Bovine super-pangenome: variability (segments per bubble)”.
4. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “Bovine super-pangenome: bubble 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 (60px here).
5. Type your region of interest into the location box and press Enter.This figure is at chr23.

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

{
  "views": [
    {
      "type": "LinearGenomeView",
      "id": "bovine-chr23-lgv",
      "assembly": "bosTau9",
      "loc": "chr23",
      "tracks": [
        "bosTau9_ncbiRefSeq_ucsc",
        "bovine_bubble_score",
        {
          "trackId": "bovine_minigraph_tier",
          "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",
      "id": "bovine-chr23-lgv",
      "assembly": "bosTau9",
      "loc": "chr23",
      "tracks": [
        "bosTau9_ncbiRefSeq_ucsc",
        "bovine_bubble_score",
        {
          "trackId": "bovine_minigraph_tier",
          "type": "LinearBasicDisplay",
          "showLabels": "none",
          "height": 60
        }
      ]
    }
  ]
}
JSON

cat > callouts.json <<'JSON'
[
  {
    "type": "text",
    "text": "BoLA",
    "fontSize": 18,
    "leader": true,
    "anchor": {
      "track": "bovine_bubble_score",
      "locus": "chr23:25,900,000",
      "fracY": 0.15
    },
    "dx": -100,
    "dy": -10
  }
]
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/graphgenomeview/pangenome_nonhuman.json \
  --width 1400 --height 550 \
  --timeout 300000 \
  --spec session.json --annotations callouts.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.

Opening in Desktop needs JBrowse Desktop 5.0+, and saves the view as a reopenable session.

https://jbrowse.org/code/jb2/main/?config=test_data%2Fgraphgenomeview%2Fpangenome_nonhuman.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22id%22%3A%22pangenome-bovine_bola-lgv%22%2C%22assembly%22%3A%22bosTau9%22%2C%22loc%22%3A%22chr23%3A27%2C508%2C000-27%2C536%2C000%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22bosTau9_ncbiRefSeq_ucsc%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22height%22%3A90%7D%2C%7B%22trackId%22%3A%22bovine_pangenome_vcf%22%2C%22type%22%3A%22LinearMultiSampleVariantDisplay%22%2C%22showVariantLane%22%3Atrue%2C%22height%22%3A260%7D%2C%7B%22trackId%22%3A%22bovine_minigraph_alleles%22%2C%22type%22%3A%22LinearPileupDisplay%22%2C%22height%22%3A90%7D%2C%7B%22trackId%22%3A%22bovine_minigraph_segments%22%2C%22type%22%3A%22LinearGraphDisplay%22%2C%22layoutMode%22%3A%22force%22%2C%22bubbleSpread%22%3A%22compress%22%2C%22colorScheme%22%3A%22reference-position%22%2C%22maxRegionBp%22%3A30801%2C%22height%22%3A420%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+pangenome%2Fbovine_bola

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 bosTau9, loaded from a .2bit genome.
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 “NCBI RefSeq genes (bosTau9)”.
   1. Drag the bar at the bottom edge of the track to resize it (90px 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 VCF (.vcf.gz + .tbi).This figure uses “Bovine super-pangenome variants (12 assemblies)”.
   1. Drag the bar at the bottom edge of the track to resize it (260px 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 BED (.bed.gz + .tbi).This figure uses “Bovine super-pangenome: allele inventory”.
   1. Drag the bar at the bottom edge of the track to resize it (90px here).
5. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “Bovine super-pangenome (rGFA segments)”.
   1. Track menu → Layout → Force-directed layout
   2. 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.
   3. Track menu → Color → Reference position
   4. Drag the bar at the bottom edge of the track to resize it (420px here).
6. Type your region of interest into the location box and press Enter.This figure is at chr23:27,508,000-27,536,000.

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

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 bosTau9, loaded from a .2bit genome.
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 “NCBI RefSeq genes (bosTau9)”.
   1. Drag the bar at the bottom edge of the track to resize it (90px 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 VCF (.vcf.gz + .tbi).This figure uses “Bovine super-pangenome variants (12 assemblies)”.
   1. Drag the bar at the bottom edge of the track to resize it (260px 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 BED (.bed.gz + .tbi).This figure uses “Bovine super-pangenome: allele inventory”.
   1. Drag the bar at the bottom edge of the track to resize it (90px here).
5. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “Bovine super-pangenome (rGFA segments)”.
   1. Track menu → Layout → Force-directed layout
   2. 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.
   3. Track menu → Color → Reference position
   4. Drag the bar at the bottom edge of the track to resize it (420px here).
6. Type your region of interest into the location box and press Enter.This figure is at chr23:27,508,000-27,536,000.

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

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

{
  "views": [
    {
      "type": "LinearGenomeView",
      "id": "pangenome-bovine_bola-lgv",
      "assembly": "bosTau9",
      "loc": "chr23:27,508,000-27,536,000",
      "tracks": [
        {
          "trackId": "bosTau9_ncbiRefSeq_ucsc",
          "type": "LinearBasicDisplay",
          "height": 90
        },
        {
          "trackId": "bovine_pangenome_vcf",
          "type": "LinearMultiSampleVariantDisplay",
          "showVariantLane": true,
          "height": 260
        },
        {
          "trackId": "bovine_minigraph_alleles",
          "type": "LinearPileupDisplay",
          "height": 90
        },
        {
          "trackId": "bovine_minigraph_segments",
          "type": "LinearGraphDisplay",
          "layoutMode": "force",
          "bubbleSpread": "compress",
          "colorScheme": "reference-position",
          "maxRegionBp": 30801,
          "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'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "id": "pangenome-bovine_bola-lgv",
      "assembly": "bosTau9",
      "loc": "chr23:27,508,000-27,536,000",
      "tracks": [
        {
          "trackId": "bosTau9_ncbiRefSeq_ucsc",
          "type": "LinearBasicDisplay",
          "height": 90
        },
        {
          "trackId": "bovine_pangenome_vcf",
          "type": "LinearMultiSampleVariantDisplay",
          "showVariantLane": true,
          "height": 260
        },
        {
          "trackId": "bovine_minigraph_alleles",
          "type": "LinearPileupDisplay",
          "height": 90
        },
        {
          "trackId": "bovine_minigraph_segments",
          "type": "LinearGraphDisplay",
          "layoutMode": "force",
          "bubbleSpread": "compress",
          "colorScheme": "reference-position",
          "maxRegionBp": 30801,
          "height": 420
        }
      ]
    }
  ]
}
JSON

cat > callouts.json <<'JSON'
[
  {
    "type": "text",
    "text": "graph alleles, each sequence once, whichever assemblies have it",
    "fontSize": 18,
    "leader": true,
    "anchor": {
      "track": "bovine_minigraph_alleles",
      "locus": "chr23:27,521,000",
      "fracY": 0.45
    },
    "dx": 80,
    "dy": -10
  }
]
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/graphgenomeview/pangenome_nonhuman.json \
  --width 1400 --height 1190 \
  --timeout 300000 \
  --spec session.json --annotations callouts.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.

Opening in Desktop needs JBrowse Desktop 5.0+, and saves the view as a reopenable session.

https://jbrowse.org/code/jb2/main/?config=test_data%2Fgraphgenomeview%2Fpangenome_nonhuman.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22id%22%3A%22pangenome-bovine_polled-lgv%22%2C%22assembly%22%3A%22bosTau9%22%2C%22loc%22%3A%22chr1%3A2%2C424%2C000-2%2C436%2C000%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22omia_cattle_variants%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22height%22%3A60%7D%2C%7B%22trackId%22%3A%22bovine_pangenome_vcf%22%2C%22type%22%3A%22LinearMultiSampleVariantDisplay%22%2C%22showVariantLane%22%3Atrue%2C%22height%22%3A260%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+pangenome%2Fbovine_polled

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 bosTau9, loaded from a .2bit genome.
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 “OMIA causal variants (cattle)”.
   1. Drag the bar at the bottom edge of the track to resize it (60px 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 VCF (.vcf.gz + .tbi).This figure uses “Bovine super-pangenome variants (12 assemblies)”.
   1. Drag the bar at the bottom edge of the track to resize it (260px here).
4. Type your region of interest into the location box and press Enter.This figure is at chr1:2,424,000-2,436,000.

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

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 bosTau9, loaded from a .2bit genome.
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 “OMIA causal variants (cattle)”.
   1. Drag the bar at the bottom edge of the track to resize it (60px 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 VCF (.vcf.gz + .tbi).This figure uses “Bovine super-pangenome variants (12 assemblies)”.
   1. Drag the bar at the bottom edge of the track to resize it (260px here).
4. Type your region of interest into the location box and press Enter.This figure is at chr1:2,424,000-2,436,000.

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

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

{
  "views": [
    {
      "type": "LinearGenomeView",
      "id": "pangenome-bovine_polled-lgv",
      "assembly": "bosTau9",
      "loc": "chr1:2,424,000-2,436,000",
      "tracks": [
        {
          "trackId": "omia_cattle_variants",
          "type": "LinearBasicDisplay",
          "height": 60
        },
        {
          "trackId": "bovine_pangenome_vcf",
          "type": "LinearMultiSampleVariantDisplay",
          "showVariantLane": true,
          "height": 260
        }
      ]
    }
  ]
}

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/pangenome_nonhuman.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearGenomeView",
            "id": "pangenome-bovine_polled-lgv",
            "assembly": "bosTau9",
            "loc": "chr1:2,424,000-2,436,000",
            "tracks": [
                {
                    "trackId": "omia_cattle_variants",
                    "type": "LinearBasicDisplay",
                    "height": 60
                },
                {
                    "trackId": "bovine_pangenome_vcf",
                    "type": "LinearMultiSampleVariantDisplay",
                    "showVariantLane": True,
                    "height": 260
                }
            ]
        }
    ],
)
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/code/jb2/main/test_data/graphgenomeview/pangenome_nonhuman.json \
  --assembly bosTau9 --loc chr1:2,424,000-2,436,000 \
  --track omia_cattle_variants display:LinearBasicDisplay '{"height":60}' \
  --track bovine_pangenome_vcf display:LinearMultiSampleVariantDisplay '{"showVariantLane":true,"height":260}' \
  --width 1400 --out figure.svg

It has no flag for this figure's id, 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",
      "id": "pangenome-bovine_polled-lgv",
      "assembly": "bosTau9",
      "loc": "chr1:2,424,000-2,436,000",
      "tracks": [
        {
          "trackId": "omia_cattle_variants",
          "type": "LinearBasicDisplay",
          "height": 60
        },
        {
          "trackId": "bovine_pangenome_vcf",
          "type": "LinearMultiSampleVariantDisplay",
          "showVariantLane": true,
          "height": 260
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/graphgenomeview/pangenome_nonhuman.json \
  --width 1400 --height 580 \
  --timeout 300000 \
  --spec 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.

Opening in Desktop needs JBrowse Desktop 5.0+, and saves the view as a reopenable session.

https://jbrowse.org/code/jb2/main/?config=test_data%2Fgraphgenomeview%2Fpangenome_nonhuman.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22id%22%3A%22pangenome-bovine_kit-lgv%22%2C%22assembly%22%3A%22bosTau9%22%2C%22loc%22%3A%22chr6%3A70%2C080%2C000-70%2C180%2C000%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22bosTau9_ncbiRefSeq_ucsc%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22height%22%3A90%7D%2C%7B%22trackId%22%3A%22bovine_pangenome_vcf%22%2C%22type%22%3A%22LinearMultiSampleVariantDisplay%22%2C%22showVariantLane%22%3Atrue%2C%22height%22%3A300%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+pangenome%2Fbovine_kit

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 bosTau9, loaded from a .2bit genome.
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 “NCBI RefSeq genes (bosTau9)”.
   1. Drag the bar at the bottom edge of the track to resize it (90px 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 VCF (.vcf.gz + .tbi).This figure uses “Bovine super-pangenome variants (12 assemblies)”.
   1. Drag the bar at the bottom edge of the track to resize it (300px here).
4. Type your region of interest into the location box and press Enter.This figure is at chr6:70,080,000-70,180,000.

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

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 bosTau9, loaded from a .2bit genome.
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 “NCBI RefSeq genes (bosTau9)”.
   1. Drag the bar at the bottom edge of the track to resize it (90px 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 VCF (.vcf.gz + .tbi).This figure uses “Bovine super-pangenome variants (12 assemblies)”.
   1. Drag the bar at the bottom edge of the track to resize it (300px here).
4. Type your region of interest into the location box and press Enter.This figure is at chr6:70,080,000-70,180,000.

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

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

{
  "views": [
    {
      "type": "LinearGenomeView",
      "id": "pangenome-bovine_kit-lgv",
      "assembly": "bosTau9",
      "loc": "chr6:70,080,000-70,180,000",
      "tracks": [
        {
          "trackId": "bosTau9_ncbiRefSeq_ucsc",
          "type": "LinearBasicDisplay",
          "height": 90
        },
        {
          "trackId": "bovine_pangenome_vcf",
          "type": "LinearMultiSampleVariantDisplay",
          "showVariantLane": true,
          "height": 300
        }
      ]
    }
  ]
}

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/pangenome_nonhuman.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearGenomeView",
            "id": "pangenome-bovine_kit-lgv",
            "assembly": "bosTau9",
            "loc": "chr6:70,080,000-70,180,000",
            "tracks": [
                {
                    "trackId": "bosTau9_ncbiRefSeq_ucsc",
                    "type": "LinearBasicDisplay",
                    "height": 90
                },
                {
                    "trackId": "bovine_pangenome_vcf",
                    "type": "LinearMultiSampleVariantDisplay",
                    "showVariantLane": True,
                    "height": 300
                }
            ]
        }
    ],
)
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/code/jb2/main/test_data/graphgenomeview/pangenome_nonhuman.json \
  --assembly bosTau9 --loc chr6:70,080,000-70,180,000 \
  --track bosTau9_ncbiRefSeq_ucsc display:LinearBasicDisplay '{"height":90}' \
  --track bovine_pangenome_vcf display:LinearMultiSampleVariantDisplay '{"showVariantLane":true,"height":300}' \
  --width 1400 --out figure.svg

It has no flag for this figure's id, 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",
      "id": "pangenome-bovine_kit-lgv",
      "assembly": "bosTau9",
      "loc": "chr6:70,080,000-70,180,000",
      "tracks": [
        {
          "trackId": "bosTau9_ncbiRefSeq_ucsc",
          "type": "LinearBasicDisplay",
          "height": 90
        },
        {
          "trackId": "bovine_pangenome_vcf",
          "type": "LinearMultiSampleVariantDisplay",
          "showVariantLane": true,
          "height": 300
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/graphgenomeview/pangenome_nonhuman.json \
  --width 1400 --height 640 \
  --timeout 300000 \
  --spec 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.

Opening in Desktop needs JBrowse Desktop 5.0+, and saves the view as a reopenable session.

https://jbrowse.org/code/jb2/main/?config=test_data%2Fgraphgenomeview%2Fpangenome_nonhuman.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22id%22%3A%22pangenome-bovine_tas2r46-lgv%22%2C%22assembly%22%3A%22bosTau9%22%2C%22loc%22%3A%22chr5%3A98%2C575%2C000-98%2C615%2C000%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22bosTau9_ncbiRefSeq_ucsc%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22height%22%3A90%7D%2C%7B%22trackId%22%3A%22bovine_pangenome_vcf%22%2C%22type%22%3A%22LinearMultiSampleVariantDisplay%22%2C%22showVariantLane%22%3Atrue%2C%22height%22%3A300%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+pangenome%2Fbovine_tas2r46

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 bosTau9, loaded from a .2bit genome.
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 “NCBI RefSeq genes (bosTau9)”.
   1. Drag the bar at the bottom edge of the track to resize it (90px 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 VCF (.vcf.gz + .tbi).This figure uses “Bovine super-pangenome variants (12 assemblies)”.
   1. Drag the bar at the bottom edge of the track to resize it (300px here).
4. Type your region of interest into the location box and press Enter.This figure is at chr5:98,575,000-98,615,000.

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

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 bosTau9, loaded from a .2bit genome.
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 “NCBI RefSeq genes (bosTau9)”.
   1. Drag the bar at the bottom edge of the track to resize it (90px 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 VCF (.vcf.gz + .tbi).This figure uses “Bovine super-pangenome variants (12 assemblies)”.
   1. Drag the bar at the bottom edge of the track to resize it (300px here).
4. Type your region of interest into the location box and press Enter.This figure is at chr5:98,575,000-98,615,000.

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

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

{
  "views": [
    {
      "type": "LinearGenomeView",
      "id": "pangenome-bovine_tas2r46-lgv",
      "assembly": "bosTau9",
      "loc": "chr5:98,575,000-98,615,000",
      "tracks": [
        {
          "trackId": "bosTau9_ncbiRefSeq_ucsc",
          "type": "LinearBasicDisplay",
          "height": 90
        },
        {
          "trackId": "bovine_pangenome_vcf",
          "type": "LinearMultiSampleVariantDisplay",
          "showVariantLane": true,
          "height": 300
        }
      ]
    }
  ]
}

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/pangenome_nonhuman.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearGenomeView",
            "id": "pangenome-bovine_tas2r46-lgv",
            "assembly": "bosTau9",
            "loc": "chr5:98,575,000-98,615,000",
            "tracks": [
                {
                    "trackId": "bosTau9_ncbiRefSeq_ucsc",
                    "type": "LinearBasicDisplay",
                    "height": 90
                },
                {
                    "trackId": "bovine_pangenome_vcf",
                    "type": "LinearMultiSampleVariantDisplay",
                    "showVariantLane": True,
                    "height": 300
                }
            ]
        }
    ],
)
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/code/jb2/main/test_data/graphgenomeview/pangenome_nonhuman.json \
  --assembly bosTau9 --loc chr5:98,575,000-98,615,000 \
  --track bosTau9_ncbiRefSeq_ucsc display:LinearBasicDisplay '{"height":90}' \
  --track bovine_pangenome_vcf display:LinearMultiSampleVariantDisplay '{"showVariantLane":true,"height":300}' \
  --width 1400 --out figure.svg

It has no flag for this figure's id, 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",
      "id": "pangenome-bovine_tas2r46-lgv",
      "assembly": "bosTau9",
      "loc": "chr5:98,575,000-98,615,000",
      "tracks": [
        {
          "trackId": "bosTau9_ncbiRefSeq_ucsc",
          "type": "LinearBasicDisplay",
          "height": 90
        },
        {
          "trackId": "bovine_pangenome_vcf",
          "type": "LinearMultiSampleVariantDisplay",
          "showVariantLane": true,
          "height": 300
        }
      ]
    }
  ]
}
JSON

cat > callouts.json <<'JSON'
[
  {
    "type": "text",
    "text": "deleted in gaur",
    "fontSize": 18,
    "leader": true,
    "anchor": {
      "track": "bovine_pangenome_vcf",
      "locus": "chr5:98,600,000",
      "fracY": 0.78
    },
    "dx": 60,
    "dy": -120
  }
]
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/graphgenomeview/pangenome_nonhuman.json \
  --width 1400 --height 640 \
  --timeout 300000 \
  --spec session.json --annotations callouts.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.