Synteny from liftOver chains (hg38 and eight vertebrates)

We look at one human locus across eight other mammals at once, from alignments that already exist. UCSC publishes a liftOver chain from hg38 to every genome it hosts, and jbrowse.org keeps each chain as an indexed alignment file. We:

• compose the chains into one multi-way synteny track, a lane per genome under the human view, each lane drawing the RefSeq gene models from that genome's UCSC hub
• stack the genomes at TP53
• pin and flip lanes near the PMP22 duplications

Prerequisites#

• htslib (tabix), to read a hosted index without downloading the alignment
• A running JBrowse instance (the web quickstart or the desktop quickstart)

# Debian/Ubuntu
sudo apt install tabix
# or conda, which has every tool above
conda install -c bioconda -c conda-forge htslib

The data#

UCSC's pairwise liftOver chains from hg38 (Kent et al. 2003), each converted to an indexed PAF and rehosted beside the hub configs genomes.jbrowse.org serves, and eight UCSC genome hubs, whose assembly entry and NCBI RefSeq gene track each lane takes verbatim.

The page's commands build local files from these, and the tracks over those read them from disk; every other track reads a hosted copy. The build script fetches everything itself. To index a chain of your own, convert it with chain2paf and make-pif, as LiftOver chains as one indexed alignment per genome shows.

LiftOver chains as one indexed alignment per genome#

A liftOver chain maps each stretch of one genome to a position in another, whether or not a gene lies there, so the track can draw each lane from the chain alone.

Each UCSC chain aligns hg38 to one other genome, so no row aligns chimpanzee to mouse. The track places each lane from the chain for that genome, and every ribbon joins a lane to hg38, whichever lane sits above it.

Each hosted file is a chain converted to PAF and indexed with jbrowse make-pif, which can write a coarser tier beside the per-base one for whole-chromosome zooms. Coarse-tier sequence names are upper-case, so tabix lists the tiers from the index without downloading the alignment.

To index a chain of your own, convert it to PAF with chain2paf, which reads an uncompressed chain, then run make-pif:

gzip -dc genomeA.genomeB.over.chain.gz > genomeA_genomeB.chain
chain2paf -i genomeA_genomeB.chain > genomeA_genomeB.paf
jbrowse make-pif genomeA_genomeB.paf

# the #pif header, if the file was built recently enough to have one
tabix -H https://jbrowse.org/ucsc/hg38/liftOver/hg38ToPanTro6.over.pif.gz | awk 'NR==1'
# how many coarse-tier sequences the index holds; zero means one tier
tabix -l https://jbrowse.org/ucsc/hg38/liftOver/hg38ToPanTro6.over.pif.gz | grep -c '^[TQ]'

Composing the chains into one track#

One SyntenyTrack names hg38 and every genome it stacks. Its adapter, a MultiPairwiseSyntenyAdapter, holds one PairwiseIndexedPAFAdapter per chain:

• Each child names its two assemblies as query,target, with the genome the chain lifts to first. The anchor is the one assembly every chain names.
• The config below is cut to a few genomes for the page, and the hosted config has all of them. genomes.jbrowse.org serves the same kind of track over every hg38 chain, which Stacking many genomes under hg38 turns on.
• The assemblies and their gene tracks come from the hub configs unchanged, and each lane finds its gene models through the session, so this track is the only addition to the hub entries.

A genome of your own loads from its FASTA instead:

{
  "name": "myGenome",
  "uri": "myGenome.fa.gz"
}

jbrowse add-assembly myGenome.fa.gz \
  --name myGenome \
  --load copy

myGenome.fa.gz
myGenome.fa.gz.fai
myGenome.fa.gz.gzi

{
  "type": "SyntenyTrack",
  "trackId": "hg38_liftover_multiway",
  "name": "hg38 vs 8 UCSC genomes (liftOver chains)",
  "assemblyNames": ["hg38", "panTro6", "rheMac10", "mm39"],
  "adapter": {
    "type": "MultiPairwiseSyntenyAdapter",
    "adapters": [
      {
        "type": "PairwiseIndexedPAFAdapter",
        "uri": "https://jbrowse.org/ucsc/hg38/liftOver/hg38ToPanTro6.over.pif.gz",
        "csi": true,
        "assemblyNames": ["panTro6", "hg38"]
      },
      {
        "type": "PairwiseIndexedPAFAdapter",
        "uri": "https://jbrowse.org/ucsc/hg38/liftOver/hg38ToRheMac10.over.pif.gz",
        "csi": true,
        "assemblyNames": ["rheMac10", "hg38"]
      },
      {
        "type": "PairwiseIndexedPAFAdapter",
        "uri": "https://jbrowse.org/ucsc/hg38/liftOver/hg38ToMm39.over.pif.gz",
        "csi": true,
        "assemblyNames": ["mm39", "hg38"]
      }
    ]
  },
  "displays": [
    {
      "type": "MultiWaySyntenyDisplay",
      "height": 600
    }
  ]
}

jbrowse add-track-json '{
  "type": "SyntenyTrack",
  "trackId": "hg38_liftover_multiway",
  "name": "hg38 vs 8 UCSC genomes (liftOver chains)",
  "assemblyNames": ["hg38", "panTro6", "rheMac10", "mm39"],
  "adapter": {
    "type": "MultiPairwiseSyntenyAdapter",
    "adapters": [
      {
        "type": "PairwiseIndexedPAFAdapter",
        "uri": "https://jbrowse.org/ucsc/hg38/liftOver/hg38ToPanTro6.over.pif.gz",
        "csi": true,
        "assemblyNames": ["panTro6", "hg38"]
      },
      {
        "type": "PairwiseIndexedPAFAdapter",
        "uri": "https://jbrowse.org/ucsc/hg38/liftOver/hg38ToRheMac10.over.pif.gz",
        "csi": true,
        "assemblyNames": ["rheMac10", "hg38"]
      },
      {
        "type": "PairwiseIndexedPAFAdapter",
        "uri": "https://jbrowse.org/ucsc/hg38/liftOver/hg38ToMm39.over.pif.gz",
        "csi": true,
        "assemblyNames": ["mm39", "hg38"]
      }
    ]
  },
  "displays": [
    {
      "type": "MultiWaySyntenyDisplay",
      "height": 600
    }
  ]
}'

{
  "type": "SyntenyTrack",
  "trackId": "hg38_liftover_multiway",
  "name": "hg38 vs 8 UCSC genomes (liftOver chains)",
  "assemblyNames": ["hg38", "panTro6", "rheMac10", "mm39"],
  "adapter": {
    "type": "MultiPairwiseSyntenyAdapter",
    "adapters": [
      {
        "type": "PairwiseIndexedPAFAdapter",
        "uri": "https://jbrowse.org/ucsc/hg38/liftOver/hg38ToPanTro6.over.pif.gz",
        "csi": true,
        "assemblyNames": ["panTro6", "hg38"]
      },
      {
        "type": "PairwiseIndexedPAFAdapter",
        "uri": "https://jbrowse.org/ucsc/hg38/liftOver/hg38ToRheMac10.over.pif.gz",
        "csi": true,
        "assemblyNames": ["rheMac10", "hg38"]
      },
      {
        "type": "PairwiseIndexedPAFAdapter",
        "uri": "https://jbrowse.org/ucsc/hg38/liftOver/hg38ToMm39.over.pif.gz",
        "csi": true,
        "assemblyNames": ["mm39", "hg38"]
      }
    ]
  },
  "displays": [
    {
      "type": "MultiWaySyntenyDisplay",
      "height": 600
    }
  ]
}

Level of detail in the track menu picks which stored tier a zoom reads, as on a pairwise synteny track. The menu offers it once every child has a coarse tier, which the tabix -l line above checks on each file.

Stacking the genomes at TP53 and at PMP22#

Opened on hg38 around TP53, the track draws a lane per genome under the human axis, each fitted to wherever its chain places the window. Each lane header names the chromosome and the span the lane shows, with [rev] where that chromosome runs the other way relative to hg38. rows.sort stacks the lanes down the tree from human, the apes first and the cow last.

{
  "defaultSession": {
    "name": "TP53 neighbourhood across nine vertebrates",
    "views": [
      {
        "type": "LinearGenomeView",
        "assembly": "hg38",
        "loc": "chr17:7,400,000-7,700,000",
        "tracks": [
          "hg38-ncbiRefSeq",
          {
            "trackId": "hg38_liftover_multiway",
            "type": "MultiWaySyntenyDisplay",
            "ribbons": { "encoding": { "color": "strand" } },
            "rows": {
              "sort": [
                "panTro6",
                "gorGor6",
                "ponAbe3",
                "rheMac10",
                "calJac4",
                "mm39",
                "canFam6",
                "bosTau9"
              ]
            },
            "height": 600
          }
        ]
      }
    ]
  }
}

jbrowse set-default-session --session - << 'EOF'
{
  "name": "TP53 neighbourhood across nine vertebrates",
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr17:7,400,000-7,700,000",
      "tracks": [
        "hg38-ncbiRefSeq",
        {
          "trackId": "hg38_liftover_multiway",
          "type": "MultiWaySyntenyDisplay",
          "ribbons": { "encoding": { "color": "strand" } },
          "rows": {
            "sort": [
              "panTro6",
              "gorGor6",
              "ponAbe3",
              "rheMac10",
              "calJac4",
              "mm39",
              "canFam6",
              "bosTau9"
            ]
          },
          "height": 600
        }
      ]
    }
  ]
}
EOF

The ribbons color by strand, the default ribbons.encoding.color (Color by... → Strand, under Ribbons in the track menu). Each ribbon takes the strand of the chain record that placed it, red where the lane runs the same way as hg38 and blue where it runs reversed.

Around TP53 every lane but gorilla places the whole window from one chain, with the same genes in the same order.

• The gorilla ribbons stop after FXR2, because gorGor6 holds the TP53 end of the window on an unplaced contig.
• The mouse, cow and dog lanes break into many ribbons, because the track cuts a chain record at every indel of 10 kb or more, which leaves gap-free runs, one ribbon each, with a gap wherever the lane has sequence hg38 lacks.
• The ape chain gaps fall under the 10 kb cut, so their ribbons look continuous.
• The mouse lane shows [rev] because its chain runs the other way against hg38 here, so its ribbons are blue.

✕

Open in JBrowse Web ↗Open in JBrowse Desktop ↗

Open in JBrowse Desktop ↗

Needs JBrowse Desktop 5.0 or newer. If nothing opens, copy the link and paste it into Desktop's Open JBrowse Web link..., on the start screen or under File → Session.

Copy

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fdemos%2Fhg38_vertebrates%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%22chr17%3A7%2C400%2C000-7%2C700%2C000%22%2C%22tracks%22%3A%5B%22hg38-ncbiRefSeq%22%2C%7B%22trackId%22%3A%22hg38_liftover_multiway%22%2C%22ribbons%22%3A%7B%22encoding%22%3A%7B%22color%22%3A%22strand%22%7D%7D%2C%22rows%22%3A%7B%22sort%22%3A%5B%22panTro6%22%2C%22gorGor6%22%2C%22ponAbe3%22%2C%22rheMac10%22%2C%22calJac4%22%2C%22mm39%22%2C%22canFam6%22%2C%22bosTau9%22%5D%7D%2C%22height%22%3A600%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+multiway_synteny%2Fhg38_vertebrates_tp53

This session loads a large dataset and takes a while to open.

Or rebuild it from your own data:

Steps

The short route: open the view in JBrowse Web, where File → Open track... adds your own files beside its hosted genome and tracks.

From scratch 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). For JBrowse Web, jbrowse add-assembly puts it in your config.json.This figure uses hg38, loaded from a .2bit genome.
2. Add a track: check one your config has in the track selector, or File → Open track... to paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “NCBI RefSeq - RefSeq All”.
3. Add the next track the same way.This figure uses “hg38 vs 8 UCSC genomes (liftOver chains)”.
   1. Track menu → Color by... → Ribbons → Strand
4. Type your region of interest into the location box and press Enter.This figure is at chr17:7,400,000-7,700,000.

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

Spec

This session spec draws the figure. It goes after &session=spec- on a JBrowse Web link that loads https://jbrowse.org/demos/hg38_vertebrates/config.json, which is what the Web button above opens.

Copy

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr17:7,400,000-7,700,000",
      "tracks": [
        "hg38-ncbiRefSeq",
        {
          "trackId": "hg38_liftover_multiway",
          "ribbons": {
            "encoding": {
              "color": "strand"
            }
          },
          "rows": {
            "sort": [
              "panTro6",
              "gorGor6",
              "ponAbe3",
              "rheMac10",
              "calJac4",
              "mm39",
              "canFam6",
              "bosTau9"
            ]
          },
          "height": 600
        }
      ]
    }
  ]
}

Notebook

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

Copy

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/demos/hg38_vertebrates/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "hg38",
            "loc": "chr17:7,400,000-7,700,000",
            "tracks": [
                "hg38-ncbiRefSeq",
                {
                    "trackId": "hg38_liftover_multiway",
                    "ribbons": {
                        "encoding": {
                            "color": "strand"
                        }
                    },
                    "rows": {
                        "sort": [
                            "panTro6",
                            "gorGor6",
                            "ponAbe3",
                            "rheMac10",
                            "calJac4",
                            "mm39",
                            "canFam6",
                            "bosTau9"
                        ]
                    },
                    "height": 600
                }
            ]
        }
    ],
)
app  # display the widget

Image

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: a data file opens as the track its name says.

Copy

npx @jbrowse/img --config https://jbrowse.org/demos/hg38_vertebrates/config.json \
  --assembly hg38 --loc chr17:7,400,000-7,700,000 \
  --track hg38-ncbiRefSeq \
  --track hg38_liftover_multiway '{"ribbons":{"encoding":{"color":"strand"}},"rows":{"sort":["panTro6","gorGor6","ponAbe3","rheMac10","calJac4","mm39","canFam6","bosTau9"]},"height":600}' \
  --width 1500 --out figure.svg

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

Agent

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit: change the location or a track's settings, or add your own track under sessionTracks, and rerun.

Copy

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr17:7,400,000-7,700,000",
      "tracks": [
        "hg38-ncbiRefSeq",
        {
          "trackId": "hg38_liftover_multiway",
          "ribbons": {
            "encoding": {
              "color": "strand"
            }
          },
          "rows": {
            "sort": [
              "panTro6",
              "gorGor6",
              "ponAbe3",
              "rheMac10",
              "calJac4",
              "mm39",
              "canFam6",
              "bosTau9"
            ]
          },
          "height": 600
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/hg38_vertebrates/config.json \
  --width 1500 --height 1000 \
  --timeout 240000 \
  --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.

Navigate to chr17:15,200,000-16,400,000, eight megabases toward the centromere, near PMP22. The region is a hotspot of segmental duplications (long repeated copies of sequence): every genome places it as several blocks, and many of those blocks run the other way against their neighbours.

A lane whose blocks mostly run backwards along hg38 draws mirrored, so its ribbons run straight on screen while the strand color still marks each of them as an inversion. Inside a lane, a ribbon crosses where one block runs against its neighbour, as in the dog and cow lanes.

A lane draws one stretch of its chromosome at a time. Where the window aligns to two stretches a window or more apart, the lane draws the one holding more of the window, and its header names the other after also at. The marmoset lane draws the reversed block that places the right of the window, and names the forward chain that places the left.

The gorilla lane header names chr17 beside chr5, the chromosome the lane drew. Part of the window aligns to chr17, the homologous chromosome, so the chr5 frame misses some of what the alignment places. Four items on the lane header menu set the frame:

• Show chr17 in this lane pins the lane onto chr17.
• Show chr5:80,472,173..81,176,598 in this lane, on the marmoset lane, pins it onto the stretch its header names.
• Flip lane turns the lane the other way on the same contig, for a lane whose blocks split about evenly between the two orientations.
• Let the lane choose its orientation hands the choice back.

✕

Open in JBrowse Web ↗Open in JBrowse Desktop ↗

Open in JBrowse Desktop ↗

Needs JBrowse Desktop 5.0 or newer. If nothing opens, copy the link and paste it into Desktop's Open JBrowse Web link..., on the start screen or under File → Session.

Copy

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fdemos%2Fhg38_vertebrates%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%22chr17%3A15%2C200%2C000-16%2C400%2C000%22%2C%22tracks%22%3A%5B%22hg38-ncbiRefSeq%22%2C%7B%22trackId%22%3A%22hg38_liftover_multiway%22%2C%22ribbons%22%3A%7B%22encoding%22%3A%7B%22color%22%3A%22strand%22%7D%7D%2C%22rows%22%3A%7B%22sort%22%3A%5B%22panTro6%22%2C%22gorGor6%22%2C%22ponAbe3%22%2C%22rheMac10%22%2C%22calJac4%22%2C%22mm39%22%2C%22canFam6%22%2C%22bosTau9%22%5D%7D%2C%22height%22%3A600%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+multiway_synteny%2Fhg38_vertebrates_17p_strand

This session loads a large dataset and takes a while to open.

Or rebuild it from your own data:

Steps

The short route: open the view in JBrowse Web, where File → Open track... adds your own files beside its hosted genome and tracks.

From scratch 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). For JBrowse Web, jbrowse add-assembly puts it in your config.json.This figure uses hg38, loaded from a .2bit genome.
2. Add a track: check one your config has in the track selector, or File → Open track... to paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “NCBI RefSeq - RefSeq All”.
3. Add the next track the same way.This figure uses “hg38 vs 8 UCSC genomes (liftOver chains)”.
   1. Track menu → Color by... → Ribbons → Strand
4. Type your region of interest into the location box and press Enter.This figure is at chr17:15,200,000-16,400,000.

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

Spec

This session spec draws the figure. It goes after &session=spec- on a JBrowse Web link that loads https://jbrowse.org/demos/hg38_vertebrates/config.json, which is what the Web button above opens.

Copy

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr17:15,200,000-16,400,000",
      "tracks": [
        "hg38-ncbiRefSeq",
        {
          "trackId": "hg38_liftover_multiway",
          "ribbons": {
            "encoding": {
              "color": "strand"
            }
          },
          "rows": {
            "sort": [
              "panTro6",
              "gorGor6",
              "ponAbe3",
              "rheMac10",
              "calJac4",
              "mm39",
              "canFam6",
              "bosTau9"
            ]
          },
          "height": 600
        }
      ]
    }
  ]
}

Notebook

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

Copy

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/demos/hg38_vertebrates/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "hg38",
            "loc": "chr17:15,200,000-16,400,000",
            "tracks": [
                "hg38-ncbiRefSeq",
                {
                    "trackId": "hg38_liftover_multiway",
                    "ribbons": {
                        "encoding": {
                            "color": "strand"
                        }
                    },
                    "rows": {
                        "sort": [
                            "panTro6",
                            "gorGor6",
                            "ponAbe3",
                            "rheMac10",
                            "calJac4",
                            "mm39",
                            "canFam6",
                            "bosTau9"
                        ]
                    },
                    "height": 600
                }
            ]
        }
    ],
)
app  # display the widget

Image

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: a data file opens as the track its name says.

Copy

npx @jbrowse/img --config https://jbrowse.org/demos/hg38_vertebrates/config.json \
  --assembly hg38 --loc chr17:15,200,000-16,400,000 \
  --track hg38-ncbiRefSeq \
  --track hg38_liftover_multiway '{"ribbons":{"encoding":{"color":"strand"}},"rows":{"sort":["panTro6","gorGor6","ponAbe3","rheMac10","calJac4","mm39","canFam6","bosTau9"]},"height":600}' \
  --width 1500 --out figure.svg

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

Agent

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit: change the location or a track's settings, or add your own track under sessionTracks, and rerun.

Copy

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr17:15,200,000-16,400,000",
      "tracks": [
        "hg38-ncbiRefSeq",
        {
          "trackId": "hg38_liftover_multiway",
          "ribbons": {
            "encoding": {
              "color": "strand"
            }
          },
          "rows": {
            "sort": [
              "panTro6",
              "gorGor6",
              "ponAbe3",
              "rheMac10",
              "calJac4",
              "mm39",
              "canFam6",
              "bosTau9"
            ]
          },
          "height": 600
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/hg38_vertebrates/config.json \
  --width 1500 --height 1000 \
  --timeout 240000 \
  --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.

Reproduce it end to end#

The script writes one config, with nothing to build or upload, in three steps:

1. Probe which of the listed genomes have both a hub config and an indexed chain with its .csi on jbrowse.org, and drop the rest.
2. Report the tiers each chain file holds, since Level of detail needs a coarse tier in every child.
3. Write each kept genome's hub entry and gene track, and one composed track with a child per chain.

GENOMES picks a different set; see Prerequisites.

curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/build_hg38_liftover_multiway.sh
bash build_hg38_liftover_multiway.sh   # writes ./hg38_vertebrates_build/config.json

See also#

• Tutorial: Pangenome (HPRC) part 2: haplotypes against each other
• Tutorial: Synteny from gene symbols (eight primates)
• Tutorial: Synteny from a Cactus alignment (T2T apes)
• Tutorial: Synteny from gene symbols (E. coli genomes)
• Tutorial: Synteny on genomes.jbrowse.org
• Tutorial: Synteny visualization (all-vs-all minimap2)
• Tutorial: Synteny on a circle (human and mouse)
• User guide: Multi-way synteny display

External links#

• UCSC Genome Browser downloads: https://hgdownload.soe.ucsc.edu/downloads.html

Citations#

• Kent et al. (2003). Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes

Feedback on this tutorial is welcome: contact us.