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Synteny from gene symbols (eight primates)

TL;DR: we look at one human locus across seven other primates at once, without aligning any of the genomes. NCBI gives an orthologous gene the same symbol in every species it annotates, so an ortholog table is a join on the gene name, built from eight GFF3 files in seconds. Each primate then becomes a lane under the human view, in its own coordinates, carrying its own gene models. A gene family whose copies got placeholder names is what the join cannot see, and the page ends there.

Prerequisites

Where the data comes from

Eight RefSeq assemblies, each fetched by accession with the datasets CLI: the current human reference, the six NHGRI telomere-to-telomere ape assemblies (Yoo et al. 2025) and the telomere-to-telomere rhesus macaque.

An ortholog table without an aligner

The grape, peach and cacao page builds its ortholog table by aligning coding sequence, and the OrthoFinder page by clustering proteins. Both produce the same .blocks shape: one row per orthologous group, one column per genome, a gene id in each cell. For genomes annotated by one pipeline there is a third way to fill that table. NCBI's eukaryotic annotation pipeline names a gene after its ortholog, so human TP53 is chimpanzee TP53 and gorilla TP53, and the table is a join on the Name attribute of each GFF3.

The join needs only the annotations, so the download is a GFF3 and a sequence report per genome:

# one RefSeq accession per line; the first is the genome the rows are anchored on
datasets download genome accession --inputfile accessions.txt \
  --include gff3,seq-report --filename genomes.zip
unzip genomes.zip

symbols_to_blocks.py reads each GFF3 once, writes a BED of its protein-coding genes and the table, and prints the column order it used:

curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/symbols_to_blocks.py
# --anchor names the genome whose genes are the rows; every other column is
# that gene's ortholog, or a dot
python3 symbols_to_blocks.py --anchor human -o primates.blocks \
  human=human.gff.gz chimp=chimp.gff.gz bonobo=bonobo.gff.gz gorilla=gorilla.gff.gz \
  sumatran=sumatran.gff.gz bornean=bornean.gff.gz siamang=siamang.gff.gz macaque=macaque.gff.gz

Symbols are compared case-folded, so a mouse Atp5f1a would meet the human ATP5F1A, and a gene whose name is an NCBI LOC placeholder joins nothing. A symbol appearing twice in one genome is a paralog and the first copy in file order takes the cell. The helper prints how much of each column it filled; for these eight the lanes come back nearly full, because the annotations share one naming pipeline.

Setting up the assemblies

The lanes never read sequence, so each assembly is the chromosome lengths from the sequence report, with the same report as its alias table so chr17 resolves to NC_000017.11:

# the four columns NcbiSequenceReportAliasAdapter reads
dataformat tsv genome-seq --package genomes.zip \
  --inputfile GCF_000001405.40/sequence_report.jsonl \
  --fields genbank-seq-acc,refseq-seq-acc,sequence-name,ucsc-style-name \
  > human.sequence_report.tsv
{
  "name": "human",
  "displayName": "Human (GRCh38.p14)",
  "sequence": {
    "type": "ReferenceSequenceTrack",
    "trackId": "human-ReferenceSequenceTrack",
    "adapter": {
      "type": "ChromSizesAdapter",
      "chromSizesLocation": { "uri": "human.chrom.sizes" }
    }
  },
  "refNameAliases": {
    "adapter": {
      "type": "NcbiSequenceReportAliasAdapter",
      "location": { "uri": "human.sequence_report.tsv" }
    }
  }
}

Each GFF3, filtered to the assembled chromosomes, sorted, bgzipped and tabix-indexed as in the web quickstart, is that genome's gene track. A lane finds its gene models through the session, so the track only has to exist under the lane's assembly name.

The ortholog track

One SyntenyTrack names all eight assemblies. blockAssemblies and bedLocations are positional against the table's columns, in the order the helper printed. The display colors a gene by its symbol, so a conserved gene is one color down the whole stack and a lane missing it breaks the column:

{
  "type": "SyntenyTrack",
  "trackId": "primate_orthologs",
  "name": "Primate orthologs by gene symbol (8 genomes, RefSeq)",
  "assemblyNames": [
    "human",
    "chimp",
    "bonobo",
    "gorilla",
    "sumatran",
    "bornean",
    "siamang",
    "macaque"
  ],
  "adapter": {
    "type": "MCScanBlocksAdapter",
    "mcscanBlocksLocation": { "uri": "primates.blocks" },
    "blockAssemblies": [
      "human",
      "chimp",
      "bonobo",
      "gorilla",
      "sumatran",
      "bornean",
      "siamang",
      "macaque"
    ],
    "bedLocations": [
      { "uri": "human.bed" },
      { "uri": "chimp.bed" },
      { "uri": "bonobo.bed" },
      { "uri": "gorilla.bed" },
      { "uri": "sumatran.bed" },
      { "uri": "bornean.bed" },
      { "uri": "siamang.bed" },
      { "uri": "macaque.bed" }
    ],
    "assemblyNames": [
      "human",
      "chimp",
      "bonobo",
      "gorilla",
      "sumatran",
      "bornean",
      "siamang",
      "macaque"
    ]
  },
  "displays": [
    {
      "type": "MultiWaySyntenyDisplay",
      "displayId": "primate_orthologs-MultiWaySyntenyDisplay",
      "color": "jexl:feature.name ? randomColor(feature.name) : '#b0b0b0'"
    }
  ]
}
jbrowse add-track-json '{
  "type": "SyntenyTrack",
  "trackId": "primate_orthologs",
  "name": "Primate orthologs by gene symbol (8 genomes, RefSeq)",
  "assemblyNames": [
    "human",
    "chimp",
    "bonobo",
    "gorilla",
    "sumatran",
    "bornean",
    "siamang",
    "macaque"
  ],
  "adapter": {
    "type": "MCScanBlocksAdapter",
    "mcscanBlocksLocation": { "uri": "primates.blocks" },
    "blockAssemblies": [
      "human",
      "chimp",
      "bonobo",
      "gorilla",
      "sumatran",
      "bornean",
      "siamang",
      "macaque"
    ],
    "bedLocations": [
      { "uri": "human.bed" },
      { "uri": "chimp.bed" },
      { "uri": "bonobo.bed" },
      { "uri": "gorilla.bed" },
      { "uri": "sumatran.bed" },
      { "uri": "bornean.bed" },
      { "uri": "siamang.bed" },
      { "uri": "macaque.bed" }
    ],
    "assemblyNames": [
      "human",
      "chimp",
      "bonobo",
      "gorilla",
      "sumatran",
      "bornean",
      "siamang",
      "macaque"
    ]
  },
  "displays": [
    {
      "type": "MultiWaySyntenyDisplay",
      "displayId": "primate_orthologs-MultiWaySyntenyDisplay",
      "color": "jexl:feature.name ? randomColor(feature.name) : '\''#b0b0b0'\''"
    }
  ]
}'

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

{
  "type": "SyntenyTrack",
  "trackId": "primate_orthologs",
  "name": "Primate orthologs by gene symbol (8 genomes, RefSeq)",
  "assemblyNames": [
    "human",
    "chimp",
    "bonobo",
    "gorilla",
    "sumatran",
    "bornean",
    "siamang",
    "macaque"
  ],
  "adapter": {
    "type": "MCScanBlocksAdapter",
    "mcscanBlocksLocation": { "uri": "primates.blocks" },
    "blockAssemblies": [
      "human",
      "chimp",
      "bonobo",
      "gorilla",
      "sumatran",
      "bornean",
      "siamang",
      "macaque"
    ],
    "bedLocations": [
      { "uri": "human.bed" },
      { "uri": "chimp.bed" },
      { "uri": "bonobo.bed" },
      { "uri": "gorilla.bed" },
      { "uri": "sumatran.bed" },
      { "uri": "bornean.bed" },
      { "uri": "siamang.bed" },
      { "uri": "macaque.bed" }
    ],
    "assemblyNames": [
      "human",
      "chimp",
      "bonobo",
      "gorilla",
      "sumatran",
      "bornean",
      "siamang",
      "macaque"
    ]
  },
  "displays": [
    {
      "type": "MultiWaySyntenyDisplay",
      "displayId": "primate_orthologs-MultiWaySyntenyDisplay",
      "color": "jexl:feature.name ? randomColor(feature.name) : '#b0b0b0'"
    }
  ]
}

One locus, eight genomes

Opened in a linear genome view on human, the track draws a lane per genome under the human axis, each fitted to wherever that genome keeps the window's genes. A lane's header names its chromosome, the span it shows and [rev] where it reads the other way, and the ribbons between adjacent lanes join each gene to its ortholog. Color ribbons by → Strand on the track menu paints a ribbon that crosses, which is a gene running the other way relative to the lane above.

{
  "defaultSession": {
    "name": "TP53 neighbourhood across eight primates",
    "views": [
      {
        "type": "LinearGenomeView",
        "assembly": "human",
        "loc": "chr17:7,400,000-7,700,000",
        "tracks": [
          {
            "trackId": "primate_orthologs",
            "type": "MultiWaySyntenyDisplay",
            "ribbonColorBy": "strand",
            "height": 620
          }
        ]
      }
    ]
  }
}
jbrowse set-default-session --session - << 'EOF'
{
  "name": "TP53 neighbourhood across eight primates",
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "human",
      "loc": "chr17:7,400,000-7,700,000",
      "tracks": [
        {
          "trackId": "primate_orthologs",
          "type": "MultiWaySyntenyDisplay",
          "ribbonColorBy": "strand",
          "height": 620
        }
      ]
    }
  ]
}
EOF

Open this session in JBrowse

The TP53 neighbourhood on human chr17 over seven primate lanes from one gene-symbol ortholog track, each lane drawing its own RefSeq gene models on its own chromosome. Every lane keeps the block in order; the siamang lane reads it reversed, and its ribbons are the crossed ones. 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 human.
  2. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses the “primate_orthologs” track.
  3. Track menu → Color ribbons by → Strand
  4. Drag the bar at the bottom edge of the track to resize it.
  5. Type your region of interest into the location box and press Enter.This figure is at chr17:7,400,000-7,700,000.

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%2Fdemos%2Fprimate_orthologs%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22human%22%2C%22loc%22%3A%22chr17%3A7%2C400%2C000-7%2C700%2C000%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22primate_orthologs%22%2C%22type%22%3A%22MultiWaySyntenyDisplay%22%2C%22ribbonColorBy%22%3A%22strand%22%2C%22height%22%3A620%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+multiway_synteny%2Fprimate_tp53_lanes

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

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "human",
      "loc": "chr17:7,400,000-7,700,000",
      "tracks": [
        {
          "trackId": "primate_orthologs",
          "type": "MultiWaySyntenyDisplay",
          "ribbonColorBy": "strand",
          "height": 620
        }
      ]
    }
  ]
}

Loaded against config: https://jbrowse.org/demos/primate_orthologs/config.json

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

from jbrowse_anywidget import LinearGenomeView, make_assembly

view = LinearGenomeView(
    assembly=make_assembly("human", "https://your-server/your-genome.fa.gz"),
    location="chr17:7,400,000-7,700,000",
)

view.add_track({
    "type": "FeatureTrack",
    "trackId": "my_track",
    "name": "My track",
    "assemblyNames": ["human"],
    "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": "human",
      "loc": "chr17:7,400,000-7,700,000",
      "tracks": [
        {
          "trackId": "primate_orthologs",
          "type": "MultiWaySyntenyDisplay",
          "ribbonColorBy": "strand",
          "height": 620
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/primate_orthologs/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.

Zoomed out to ten megabases the same track reads as a synteny painting. The ribbons bundle where gene order is shared and cross where a block is inverted in one lineage, and a lane whose header carries a multiple is holding the same genes over more sequence.

Ten megabases of human chr17 over the seven primate lanes, ribbons colored by strand. Most of the window is straight ribbons; the crossed bundles are blocks inverted in one lane relative to the one above it. 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 human.
  2. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses the “primate_orthologs” track.
  3. Track menu → Color ribbons by → Strand
  4. Drag the bar at the bottom edge of the track to resize it.
  5. Type your region of interest into the location box and press Enter.This figure is at chr17:40,000,000-50,000,000.

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%2Fdemos%2Fprimate_orthologs%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22human%22%2C%22loc%22%3A%22chr17%3A40%2C000%2C000-50%2C000%2C000%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22primate_orthologs%22%2C%22type%22%3A%22MultiWaySyntenyDisplay%22%2C%22ribbonColorBy%22%3A%22strand%22%2C%22height%22%3A620%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+multiway_synteny%2Fprimate_chr17_inversions

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

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "human",
      "loc": "chr17:40,000,000-50,000,000",
      "tracks": [
        {
          "trackId": "primate_orthologs",
          "type": "MultiWaySyntenyDisplay",
          "ribbonColorBy": "strand",
          "height": 620
        }
      ]
    }
  ]
}

Loaded against config: https://jbrowse.org/demos/primate_orthologs/config.json

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

from jbrowse_anywidget import LinearGenomeView, make_assembly

view = LinearGenomeView(
    assembly=make_assembly("human", "https://your-server/your-genome.fa.gz"),
    location="chr17:40,000,000-50,000,000",
)

view.add_track({
    "type": "FeatureTrack",
    "trackId": "my_track",
    "name": "My track",
    "assemblyNames": ["human"],
    "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": "human",
      "loc": "chr17:40,000,000-50,000,000",
      "tracks": [
        {
          "trackId": "primate_orthologs",
          "type": "MultiWaySyntenyDisplay",
          "ribbonColorBy": "strand",
          "height": 620
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/primate_orthologs/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.

A window across a chromosome fusion

Human chromosome 2 is two ape chromosomes joined end to end. A window over the fusion point has orthologs on both of them, and a lane can follow one contig at a time, so each ape lane picks the one holding more of the window's genes. A lane whose other chromosome still holds a fair share of the window names it in its header, and Show ⟨contig⟩ in this lane on the header menu swaps the lane onto it. The genes on the other side of the fusion keep their models in every lane and have no ribbon.

Three megabases of human chr2 across the 2q13 fusion point over the seven primate lanes. Every non-human lane sits on the chromosome holding most of the window, and the three African ape lanes name the other in their headers; the genes past the fusion have models in every lane and ribbons in none. 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 human.
  2. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses the “primate_orthologs” track.
  3. Drag the bar at the bottom edge of the track to resize it.
  4. Type your region of interest into the location box and press Enter.This figure is at chr2:112,500,000-115,500,000.

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%2Fdemos%2Fprimate_orthologs%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22human%22%2C%22loc%22%3A%22chr2%3A112%2C500%2C000-115%2C500%2C000%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22primate_orthologs%22%2C%22type%22%3A%22MultiWaySyntenyDisplay%22%2C%22height%22%3A620%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+multiway_synteny%2Fprimate_chr2_fusion

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

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "human",
      "loc": "chr2:112,500,000-115,500,000",
      "tracks": [
        {
          "trackId": "primate_orthologs",
          "type": "MultiWaySyntenyDisplay",
          "height": 620
        }
      ]
    }
  ]
}

Loaded against config: https://jbrowse.org/demos/primate_orthologs/config.json

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

from jbrowse_anywidget import LinearGenomeView, make_assembly

view = LinearGenomeView(
    assembly=make_assembly("human", "https://your-server/your-genome.fa.gz"),
    location="chr2:112,500,000-115,500,000",
)

view.add_track({
    "type": "FeatureTrack",
    "trackId": "my_track",
    "name": "My track",
    "assemblyNames": ["human"],
    "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": "human",
      "loc": "chr2:112,500,000-115,500,000",
      "tracks": [
        {
          "trackId": "primate_orthologs",
          "type": "MultiWaySyntenyDisplay",
          "height": 620
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/primate_orthologs/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.

What a symbol join cannot see

The join is exactly as good as the naming. The salivary amylase cluster on human chr1 is a run of near-identical copies whose human names are lettered (AMY1A, AMY1B, AMY1C), while the other primates' copies were left as placeholder LOC ids, so the table holds no row for them. Every lane still draws its own copies, from its own annotation, and the ribbons stop at the cluster's edge.

The amylase cluster on human chr1 over the seven primate lanes. The flanking genes chain down the stack; the amylase copies in each lane are drawn from that genome's annotation and joined to nothing. 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 human.
  2. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses the “primate_orthologs” track.
  3. Drag the bar at the bottom edge of the track to resize it.
  4. Type your region of interest into the location box and press Enter.This figure is at chr1:103,500,000-103,800,000.

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%2Fdemos%2Fprimate_orthologs%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22human%22%2C%22loc%22%3A%22chr1%3A103%2C500%2C000-103%2C800%2C000%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22primate_orthologs%22%2C%22type%22%3A%22MultiWaySyntenyDisplay%22%2C%22height%22%3A620%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+multiway_synteny%2Fprimate_amy_cluster

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

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "human",
      "loc": "chr1:103,500,000-103,800,000",
      "tracks": [
        {
          "trackId": "primate_orthologs",
          "type": "MultiWaySyntenyDisplay",
          "height": 620
        }
      ]
    }
  ]
}

Loaded against config: https://jbrowse.org/demos/primate_orthologs/config.json

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

from jbrowse_anywidget import LinearGenomeView, make_assembly

view = LinearGenomeView(
    assembly=make_assembly("human", "https://your-server/your-genome.fa.gz"),
    location="chr1:103,500,000-103,800,000",
)

view.add_track({
    "type": "FeatureTrack",
    "trackId": "my_track",
    "name": "My track",
    "assemblyNames": ["human"],
    "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": "human",
      "loc": "chr1:103,500,000-103,800,000",
      "tracks": [
        {
          "trackId": "primate_orthologs",
          "type": "MultiWaySyntenyDisplay",
          "height": 620
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/primate_orthologs/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.

For a locus like this the table wants a real homology call, which is what the OrthoFinder page builds, or an alignment.

Reproduce it end to end

The script fetches the eight annotations, builds the table and writes the config; see Prerequisites.

curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/build_primate_orthologs.sh
bash build_primate_orthologs.sh

See also

References