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Synteny on genomes.jbrowse.org

TL;DR: genomes.jbrowse.org already carries UCSC's pairwise liftOver alignments for every genome, so you can turn one on in a linear genome view and launch a two-panel linear synteny view from any chain block. JBrowse resolves the mate genome on demand, so the second assembly needs no setup.

Prerequisites

  • nothing to install: this is a click-path through a hosted site, and no data, config or second assembly is prepared by hand

Where the data comes from

genomes.jbrowse.org's own hosted configs for the three genomes this page compares, each already carrying UCSC's pairwise liftOver chains to the others.

The hosted configs

genomes.jbrowse.org hosts a config for every UCSC genome, each carrying UCSC's pairwise liftOver alignments to the others. This page compares hg38 against T2T-CHM13 (hs1) at TNNT3, a locus the two lay out differently.

Opening a liftOver track

Open hg38 on genomes.jbrowse.org, find Pairwise alignments → liftOver in the track selector and turn on hg38 to Human (hs1) liftOver. Type TNNT3 into the location box; the hosted config ships a name index.

The hg38 config declares only hg38. A track referencing an assembly JBrowse does not know is resolved through the Core-handleUnrecognizedAssembly extension point, where the site's hub plugin supplies the mate genome's config.

In a plain linear genome view the liftOver track draws one feature per chain block, laid out in rows.

Launching a synteny view

Right-click any chain block and choose Linear synteny view with ..., which names the other assembly. The dialog frames the second panel. Use CIGAR to map the current visible region to the target walks the alignment to find the interval matching what is in view; the chain through TNNT3 spans the chromosome, so unticked it frames both panels on all of chromosome 11. A reverse-strand block adds Horizontally flip inverted targets, ticked by default.

Open in new view appends the result below the linear view; Replace current view puts it in that view's place.

Launching from a chain block on the hg38 to Human (hs1) liftOver track at TNNT3: the block's right-click menu, the dialog that frames the second panel, and Replace current view putting the two-panel synteny view in the linear view's place. The hg38 panel arrives carrying the gene track that was open above; the hs1 panel arrives empty. Open the session this video starts in ↗

The panel you launched from keeps the tracks that view had on (Copy this view's tracks into its panel turns that off). The hs1 panel opens empty; the view header's track selector button lists one selector per panel.

A locus no single chain block covers takes a second route: drag-select it on the scale bar and pick Launch → Linear synteny view, whose dialog offers every assembly the session's synteny datasets align to it. See the linear synteny view guide.

Ribbon display settings

Two settings live in the synteny view's settings menu, the sliders button in its header:

  • Curved lines draws each ribbon as a curve, easier to follow across a gap
  • CIGAR indels → Transparent indels leaves insertions and deletions inside each block as see-through gaps

The palette button in the same header sets what ribbons are colored by. Strand paints each block by its orientation, and is what the figures below use.

The same TNNT3 comparison before and after both settings, with the menu that holds them open on top. Top: straight ribbons with colored indels. Bottom: curved ribbons with transparent indels. Open in JBrowse: As it opens ↗ (large dataset — this session takes a while to load) · Curved + transparent indels ↗ (large dataset — this session takes a while to load)

The steps behind the figure above, run against your own data.

  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: hg38, hs1.
  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 “hg38 vs T2T-CHM13 (UCSC liftOver)”.
  4. Click Launch.
  5. Synteny view header → palette button → StrandThe palette button's tooltip reads "Color by: ...".
  6. 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).Row 1 (hg38) — This figure uses “NCBI RefSeq genes”.
  7. Track menu → Gene glyph → Representative transcriptRow 1 (hg38).
  8. Type your region of interest into the location box and press Enter.Row 1 (hg38) — This figure is at chr11:1,881,000-1,955,000.
  9. View menu → Show... → OffsetRow 1 (hg38).
  10. 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).Row 2 (hs1) — This figure uses “NCBI RefSeq genes”.
  11. Track menu → Gene glyph → Representative transcriptRow 2 (hs1).
  12. Track menu → Show only genes (checked)Row 2 (hs1).
  13. Type your region of interest into the location box and press Enter.Row 2 (hs1) — This figure is at chr11:1,964,700-2,038,700.
  14. View menu → Show... → OffsetRow 2 (hs1).

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=test_data%2Fhg38_hs1_synteny%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearSyntenyView%22%2C%22colorBy%22%3A%22strand%22%2C%22tracks%22%3A%5B%5B%22hg38_hs1_synteny%22%5D%5D%2C%22views%22%3A%5B%7B%22assembly%22%3A%22hg38%22%2C%22loc%22%3A%22chr11%3A1%2C881%2C000-1%2C955%2C000%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22hg38-genes%22%2C%22geneGlyphMode%22%3A%22longestCoding%22%7D%5D%2C%22trackLabels%22%3A%22offset%22%7D%2C%7B%22assembly%22%3A%22hs1%22%2C%22loc%22%3A%22chr11%3A1%2C964%2C700-2%2C038%2C700%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22hs1-genes%22%2C%22geneGlyphMode%22%3A%22longestCoding%22%2C%22showOnlyGenes%22%3Atrue%7D%5D%2C%22trackLabels%22%3A%22offset%22%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+genomes_synteny%2Fribbons_default

This session spec pastes after &session=spec- on any JBrowse Web instance.

{
  "views": [
    {
      "type": "LinearSyntenyView",
      "colorBy": "strand",
      "tracks": [
        [
          "hg38_hs1_synteny"
        ]
      ],
      "views": [
        {
          "assembly": "hg38",
          "loc": "chr11:1,881,000-1,955,000",
          "tracks": [
            {
              "trackId": "hg38-genes",
              "geneGlyphMode": "longestCoding"
            }
          ],
          "trackLabels": "offset"
        },
        {
          "assembly": "hs1",
          "loc": "chr11:1,964,700-2,038,700",
          "tracks": [
            {
              "trackId": "hs1-genes",
              "geneGlyphMode": "longestCoding",
              "showOnlyGenes": true
            }
          ],
          "trackLabels": "offset"
        }
      ]
    }
  ]
}

Loaded against config: test_data/hg38_hs1_synteny/config.json

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",
      "colorBy": "strand",
      "tracks": [
        [
          "hg38_hs1_synteny"
        ]
      ],
      "views": [
        {
          "assembly": "hg38",
          "loc": "chr11:1,881,000-1,955,000",
          "tracks": [
            {
              "trackId": "hg38-genes",
              "geneGlyphMode": "longestCoding"
            }
          ],
          "trackLabels": "offset"
        },
        {
          "assembly": "hs1",
          "loc": "chr11:1,964,700-2,038,700",
          "tracks": [
            {
              "trackId": "hs1-genes",
              "geneGlyphMode": "longestCoding",
              "showOnlyGenes": true
            }
          ],
          "trackLabels": "offset"
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/hg38_hs1_synteny/config.json \
  --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 steps behind the figure above, run against your own data.

  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: hg38, hs1.
  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 “hg38 vs T2T-CHM13 (UCSC liftOver)”.
  4. Click Launch.
  5. Synteny view header → palette button → StrandThe palette button's tooltip reads "Color by: ...".
  6. Synteny display settings (the sliders button in the view header) → Curved lines (checked)
  7. Synteny display settings (the sliders button in the view header) → CIGAR indels → Transparent indelsThe row appears only when the alignments actually carry CIGAR ops — a coarse-tier PIF or a CIGAR-less PAF has none to draw.
  8. 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).Row 1 (hg38) — This figure uses “NCBI RefSeq genes”.
  9. Track menu → Gene glyph → Representative transcriptRow 1 (hg38).
  10. Type your region of interest into the location box and press Enter.Row 1 (hg38) — This figure is at chr11:1,881,000-1,955,000.
  11. View menu → Show... → OffsetRow 1 (hg38).
  12. 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).Row 2 (hs1) — This figure uses “NCBI RefSeq genes”.
  13. Track menu → Gene glyph → Representative transcriptRow 2 (hs1).
  14. Track menu → Show only genes (checked)Row 2 (hs1).
  15. Type your region of interest into the location box and press Enter.Row 2 (hs1) — This figure is at chr11:1,964,700-2,038,700.
  16. View menu → Show... → OffsetRow 2 (hs1).

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=test_data%2Fhg38_hs1_synteny%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearSyntenyView%22%2C%22colorBy%22%3A%22strand%22%2C%22tracks%22%3A%5B%5B%22hg38_hs1_synteny%22%5D%5D%2C%22drawCurves%22%3Atrue%2C%22cigarMode%22%3A%22matches%22%2C%22views%22%3A%5B%7B%22assembly%22%3A%22hg38%22%2C%22loc%22%3A%22chr11%3A1%2C881%2C000-1%2C955%2C000%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22hg38-genes%22%2C%22geneGlyphMode%22%3A%22longestCoding%22%7D%5D%2C%22trackLabels%22%3A%22offset%22%7D%2C%7B%22assembly%22%3A%22hs1%22%2C%22loc%22%3A%22chr11%3A1%2C964%2C700-2%2C038%2C700%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22hs1-genes%22%2C%22geneGlyphMode%22%3A%22longestCoding%22%2C%22showOnlyGenes%22%3Atrue%7D%5D%2C%22trackLabels%22%3A%22offset%22%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+genomes_synteny%2Fribbons_curved

This session spec pastes after &session=spec- on any JBrowse Web instance.

{
  "views": [
    {
      "type": "LinearSyntenyView",
      "colorBy": "strand",
      "tracks": [
        [
          "hg38_hs1_synteny"
        ]
      ],
      "drawCurves": true,
      "cigarMode": "matches",
      "views": [
        {
          "assembly": "hg38",
          "loc": "chr11:1,881,000-1,955,000",
          "tracks": [
            {
              "trackId": "hg38-genes",
              "geneGlyphMode": "longestCoding"
            }
          ],
          "trackLabels": "offset"
        },
        {
          "assembly": "hs1",
          "loc": "chr11:1,964,700-2,038,700",
          "tracks": [
            {
              "trackId": "hs1-genes",
              "geneGlyphMode": "longestCoding",
              "showOnlyGenes": true
            }
          ],
          "trackLabels": "offset"
        }
      ]
    }
  ]
}

Loaded against config: test_data/hg38_hs1_synteny/config.json

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",
      "colorBy": "strand",
      "tracks": [
        [
          "hg38_hs1_synteny"
        ]
      ],
      "drawCurves": true,
      "cigarMode": "matches",
      "views": [
        {
          "assembly": "hg38",
          "loc": "chr11:1,881,000-1,955,000",
          "tracks": [
            {
              "trackId": "hg38-genes",
              "geneGlyphMode": "longestCoding"
            }
          ],
          "trackLabels": "offset"
        },
        {
          "assembly": "hs1",
          "loc": "chr11:1,964,700-2,038,700",
          "tracks": [
            {
              "trackId": "hs1-genes",
              "geneGlyphMode": "longestCoding",
              "showOnlyGenes": true
            }
          ],
          "trackLabels": "offset"
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/hg38_hs1_synteny/config.json \
  --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 TNNT3 rearrangement

TNNT3 is the locus from Fig 5C of the T2T human variation paper. Against GRCh38 the region reads as an inversion plus a deletion that ablates LINC01150 in every individual; against T2T-CHM13 that segment is intact on the other side of TNNT3 in the opposite orientation. Colored by strand, it is the one off-color ribbon.

hg38 (top) vs T2T-CHM13/hs1 (bottom) at TNNT3, colored by strand with curved ribbons and transparent indels. LINC01150 sits upstream of TNNT3 in hg38 and downstream of it in T2T-CHM13, and the purple ribbon is the segment that moved. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

The steps behind the figure above, run against your own data.

  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: hg38, hs1.
  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 “hg38 vs T2T-CHM13 (UCSC liftOver)”.
  4. Click Launch.
  5. Synteny view header → palette button → StrandThe palette button's tooltip reads "Color by: ...".
  6. Synteny display settings (the sliders button in the view header) → Curved lines (checked)
  7. Synteny display settings (the sliders button in the view header) → CIGAR indels → Transparent indelsThe row appears only when the alignments actually carry CIGAR ops — a coarse-tier PIF or a CIGAR-less PAF has none to draw.
  8. 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).Row 1 (hg38) — This figure uses “NCBI RefSeq genes”.
  9. Track menu → Gene glyph → Representative transcriptRow 1 (hg38).
  10. Type your region of interest into the location box and press Enter.Row 1 (hg38) — This figure is at chr11:1,881,000-1,955,000.
  11. View menu → Show... → OffsetRow 1 (hg38).
  12. 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).Row 2 (hs1) — This figure uses “NCBI RefSeq genes”.
  13. Track menu → Gene glyph → Representative transcriptRow 2 (hs1).
  14. Track menu → Show only genes (checked)Row 2 (hs1).
  15. Type your region of interest into the location box and press Enter.Row 2 (hs1) — This figure is at chr11:1,964,700-2,038,700.
  16. View menu → Show... → OffsetRow 2 (hs1).

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=test_data%2Fhg38_hs1_synteny%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearSyntenyView%22%2C%22colorBy%22%3A%22strand%22%2C%22tracks%22%3A%5B%5B%22hg38_hs1_synteny%22%5D%5D%2C%22drawCurves%22%3Atrue%2C%22cigarMode%22%3A%22matches%22%2C%22views%22%3A%5B%7B%22assembly%22%3A%22hg38%22%2C%22loc%22%3A%22chr11%3A1%2C881%2C000-1%2C955%2C000%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22hg38-genes%22%2C%22geneGlyphMode%22%3A%22longestCoding%22%7D%5D%2C%22trackLabels%22%3A%22offset%22%7D%2C%7B%22assembly%22%3A%22hs1%22%2C%22loc%22%3A%22chr11%3A1%2C964%2C700-2%2C038%2C700%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22hs1-genes%22%2C%22geneGlyphMode%22%3A%22longestCoding%22%2C%22showOnlyGenes%22%3Atrue%7D%5D%2C%22trackLabels%22%3A%22offset%22%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+synteny_hg38_hs1_tnnt3

This session spec pastes after &session=spec- on any JBrowse Web instance.

{
  "views": [
    {
      "type": "LinearSyntenyView",
      "colorBy": "strand",
      "tracks": [
        [
          "hg38_hs1_synteny"
        ]
      ],
      "drawCurves": true,
      "cigarMode": "matches",
      "views": [
        {
          "assembly": "hg38",
          "loc": "chr11:1,881,000-1,955,000",
          "tracks": [
            {
              "trackId": "hg38-genes",
              "geneGlyphMode": "longestCoding"
            }
          ],
          "trackLabels": "offset"
        },
        {
          "assembly": "hs1",
          "loc": "chr11:1,964,700-2,038,700",
          "tracks": [
            {
              "trackId": "hs1-genes",
              "geneGlyphMode": "longestCoding",
              "showOnlyGenes": true
            }
          ],
          "trackLabels": "offset"
        }
      ]
    }
  ]
}

Loaded against config: test_data/hg38_hs1_synteny/config.json

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",
      "colorBy": "strand",
      "tracks": [
        [
          "hg38_hs1_synteny"
        ]
      ],
      "drawCurves": true,
      "cigarMode": "matches",
      "views": [
        {
          "assembly": "hg38",
          "loc": "chr11:1,881,000-1,955,000",
          "tracks": [
            {
              "trackId": "hg38-genes",
              "geneGlyphMode": "longestCoding"
            }
          ],
          "trackLabels": "offset"
        },
        {
          "assembly": "hs1",
          "loc": "chr11:1,964,700-2,038,700",
          "tracks": [
            {
              "trackId": "hs1-genes",
              "geneGlyphMode": "longestCoding",
              "showOnlyGenes": true
            }
          ],
          "trackLabels": "offset"
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/hg38_hs1_synteny/config.json \
  --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.

Trying other pairs

The same click-path works for any track under Pairwise alignments → liftOver, one per chain file UCSC publishes against the genome you are in. A close pair gives long collinear blocks, a distant one short scattered ones.

The figure below is that route on hg38 to Chimp (panTro6) liftOver, across an intron of FTO.

The four steps on the hg38-to-panTro6 liftOver track across an FTO intron: right-click a chain block, confirm the framing, launch, then add the chimp panel's genes and repeats. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

The steps behind the figure above, run against your own data.

  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 hg38.
  2. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses the “hg38-ncbiRefSeqCurated” track.
  3. Track menu → Gene glyph → Representative transcript“hg38-ncbiRefSeqCurated”.
  4. Drag the bar at the bottom edge of the track to resize it.“hg38-ncbiRefSeqCurated”.
  5. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses the “hg38-rmsk” track.
  6. Track menu → Set feature height → Compact“hg38-rmsk”.
  7. Drag the bar at the bottom edge of the track to resize it.“hg38-rmsk”.
  8. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses the “hg38_to_panTro6_liftOver” track.
  9. Track menu → Show... → Collapse groups to one row (unchecked)Offered only once the reads are grouped, since it is what the groups collapse into.“hg38_to_panTro6_liftOver”.
  10. Drag the bar at the bottom edge of the track to resize it.“hg38_to_panTro6_liftOver”.
  11. Type your region of interest into the location box and press Enter.This figure is at chr16:54,036,000-54,054,000.

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

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%2Fucsc%2Fhg38%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22hg38%22%2C%22loc%22%3A%22chr16%3A54%2C036%2C000-54%2C054%2C000%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22hg38-ncbiRefSeqCurated%22%2C%22geneGlyphMode%22%3A%22longestCoding%22%2C%22height%22%3A60%7D%2C%7B%22trackId%22%3A%22hg38-rmsk%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22displayMode%22%3A%22compact%22%2C%22height%22%3A70%7D%2C%7B%22trackId%22%3A%22hg38_to_panTro6_liftOver%22%2C%22type%22%3A%22LGVSyntenyDisplay%22%2C%22collapseGroupRows%22%3Afalse%2C%22height%22%3A60%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+genomes_synteny%2Flaunch_sequence

This session spec pastes after &session=spec- on any JBrowse Web instance.

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr16:54,036,000-54,054,000",
      "tracks": [
        {
          "trackId": "hg38-ncbiRefSeqCurated",
          "geneGlyphMode": "longestCoding",
          "height": 60
        },
        {
          "trackId": "hg38-rmsk",
          "type": "LinearBasicDisplay",
          "displayMode": "compact",
          "height": 70
        },
        {
          "trackId": "hg38_to_panTro6_liftOver",
          "type": "LGVSyntenyDisplay",
          "collapseGroupRows": false,
          "height": 60
        }
      ]
    }
  ]
}

Loaded against config: https://jbrowse.org/ucsc/hg38/config.json

The same view with jbrowse-anywidget. Point the adapter at your own file.

from jbrowse_anywidget import LinearGenomeView, fetch_hub

view = LinearGenomeView(
    assembly=fetch_hub("hg38"),
    location="chr16:54,036,000-54,054,000",
)

view.add_track({
    "type": "FeatureTrack",
    "trackId": "my_track_1",
    "name": "My track 1",
    "assemblyNames": ["hg38"],
    "adapter": {"type": "BamAdapter", "uri": "https://your-server/your-file"},
})
view.add_track({
    "type": "FeatureTrack",
    "trackId": "my_track_2",
    "name": "My track 2",
    "assemblyNames": ["hg38"],
    "adapter": {"type": "BamAdapter", "uri": "https://your-server/your-file"},
})
view.add_track({
    "type": "FeatureTrack",
    "trackId": "my_track_3",
    "name": "My track 3",
    "assemblyNames": ["hg38"],
    "adapter": {"type": "BamAdapter", "uri": "https://your-server/your-file"},
})

view  # display the widget

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

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr16:54,036,000-54,054,000",
      "tracks": [
        {
          "trackId": "hg38-ncbiRefSeqCurated",
          "geneGlyphMode": "longestCoding",
          "height": 60
        },
        {
          "trackId": "hg38-rmsk",
          "type": "LinearBasicDisplay",
          "displayMode": "compact",
          "height": 70
        },
        {
          "trackId": "hg38_to_panTro6_liftOver",
          "type": "LGVSyntenyDisplay",
          "collapseGroupRows": false,
          "height": 60
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/ucsc/hg38/config.json \
  --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.

Its last frame switches to curves and Transparent indels (above), which turns the one gap into a hole lining up against the RepeatMasker track. The element under it is an L1HS, the youngest human LINE-1 subfamily, and the chimp panel has every other repeat in the window but not that one.

The chimp panel's track selector offers NCBI RefSeq - RefSeq All and RepeatMasker, brought in with the panTro6 hub. The rest of that hub loads from File → Open connection as a JBrowse 2 hub at https://jbrowse.org/ucsc/panTro6/config.json.

To start from a gene, the site's ortholog search lists a symbol's NCBI orthologs among the hosted genomes, with a synteny view per row where an alignment exists.

See also