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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 ready-made JBrowse config for every UCSC genome, and each one already carries UCSC's pairwise liftOver alignments to the other genomes, so any pair UCSC has a chain file for can be compared in a couple of clicks.

This tutorial compares hg38 against T2T-CHM13 (hs1) at TNNT3, a locus that GRCh38 and T2T-CHM13 lay out differently.

Opening a liftOver track

Open hg38 on genomes.jbrowse.org, then in the track selector find Pairwise alignments → liftOver and turn on hg38 to Human (hs1) liftOver. Type TNNT3 into the location box to navigate to the gene; the hosted config ships a name index, so gene symbols work without any setup.

The hg38 config declares only hg38. When a track references an assembly JBrowse does not know, it asks its plugins to resolve the name (the Core-handleUnrecognizedAssembly extension point) and the site's hub plugin supplies the config, which is how every liftOver track on the site reaches its mate genome.

The liftOver track is a synteny track, and in a plain linear genome view it draws the way an alignments track does: one feature per chain block, laid out in rows.

Launching a synteny view

Right-click any chain block and choose Launch synteny view for this position. The dialog that opens controls how the second panel is framed, and its defaults suit the block you clicked. Use CIGAR to map the current visible region to the target is the option to note: JBrowse walks the alignment to find the interval matching what is in view. The chain running through TNNT3 spans the chromosome, so unticked it frames both panels on the whole of chromosome 11. A reverse-strand block adds another checkbox, Horizontally flip inverted targets, ticked by default so the target panel reads left to right.

The dialog then offers two ways out, both building the same view. Open in new view appends it below the linear view you launched from; Replace current view puts it in that view's place, which is usually what you want here, since the synteny view opens on the locus the linear view is already showing.

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 for the assembly you launched from opens with the tracks that view had on, and Copy this view's tracks into its panel in the dialog turns that off. The hs1 panel opens empty, and its tracks come from its own track selector, whose button in the view header lists one per panel.

A locus that no single chain block covers (a gene that several blocks tile, or one you have only navigated to) takes a second route: drag-select it on the scale bar and pick Launch → Linear synteny view, whose dialog picks the synteny dataset to read it from. It starts from the region, and offers every assembly the session's synteny datasets align to it, so use it when more than one liftOver track is on. See the linear synteny view guide.

Ribbon display settings

Three settings change how the ribbons read. Two are in the synteny view's settings menu, the sliders button in its header:

  • Curved lines, ticked, draws each ribbon as a curve, so a block that lands far from where it started is easier to follow across the gap.
  • CIGAR indels → Transparent indels leaves the insertions and deletions inside each block as see-through gaps, so with strand coloring on the color means one thing.

The third is the palette button further along the same header, whose menu sets what every ribbon is colored by. Strand paints each block by the orientation it landed in, and is the setting the TNNT3 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. Called against GRCh38 the region reads as a 24 kb inversion plus a 22 kb deletion that ablates LINC01150 in every individual; against T2T-CHM13 that same 22 kb is intact, just sitting on the other side of TNNT3 in the opposite orientation. Colored by strand, that segment is the one off-color ribbon in the view.

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 liftOver track under Pairwise alignments → liftOver. How much of the chain survives changes with the pair: a close comparison like hs1 or panTro6 gives long collinear blocks, a distant one short scattered ones, and the CIGAR option matters more the more diverged the pair is. That liftOver category is itself the index of which pairs exist, with one track in it per chain file UCSC publishes against the genome you are in.

The figure below is that route on hg38 to Chimp (panTro6) liftOver, across an intron of FTO, and its clicks are the ones in the clip above.

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 the ribbon to curves and to Transparent indels, both covered above, which turns the one gap in it into a hole that lines up against the RepeatMasker track over it. The element under it is an L1HS, the youngest human LINE-1 subfamily, and the chimp panel keeps every other repeat in the window but not that one.

The chimp panel's own track selector offers NCBI RefSeq - RefSeq All and RepeatMasker, because naming panTro6 also brought in the panTro6 hub's gene, repeat and gap tracks. The rest of that hub loads from File → Open connection as a JBrowse 2 hub at https://jbrowse.org/ucsc/panTro6/config.json, which is where its conservation and expression tracks are.

To start from a gene, the site's ortholog search takes a gene symbol and lists its NCBI orthologs among the hosted genomes, with a synteny view per row wherever the two assemblies have an alignment.

See also