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Rearrangements between genomes by type (SyRI)

JBrowse v5 beta

The tutorials target the JBrowse v5 beta, and the v4.3.0 release on the download page lacks some of what they show. To install the beta of JBrowse Web, run npm install -g @jbrowse/cli@next, then jbrowse create jbrowse2 --branch v5.0.0-beta.17. Desktop beta builds are coming soon.

The Columbia and Landsberg accessions of Arabidopsis thaliana differ by an inversion of more than a megabase on the short arm of chromosome 4, first seen under the microscope and later confirmed by assembling Landsberg. We find it again with SyRI, which sorts an alignment into syntenic, inverted, translocated and duplicated regions. We:

  • align six assembled accessions, run SyRI on each pair, and merge the comparisons into one PAF whose ribbons take the color of the type SyRI assigns
  • stack linear synteny views the way plotsr draws them
  • draw the same accessions as lanes of a multi-way display under Columbia coordinates

Prerequisites

# Debian/Ubuntu
sudo apt install samtools tabix minimap2
# or conda, which has every tool above
conda install -c bioconda -c conda-forge samtools htslib minimap2 \
  ncbi-datasets-cli syri
# or Linux x86_64 binaries for the tools apt lacks
wget -P ~/.local/bin \
  https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-amd64/datasets \
  https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-amd64/dataformat
chmod +x ~/.local/bin/datasets ~/.local/bin/dataformat

The data

TAIR10 for Columbia, and the chromosome-level assemblies of five more accessions from Jiao and Schneeberger 2020, the first three the ones a figure in the plotsr paper stacks.

The tracks below read local files that the build script writes from these, so run it first, or run Aligning a pair and running SyRI on chromosome-level assemblies of your own whose homologous chromosomes share a name. The script fetches everything itself.

What it isFile
Col-0, GCF_000001735.4GCF_000001735.4_TAIR10.1/
Ler, GCA_902460285.1GCA_902460285.1_Arabidopsis_thaliana_Ler/
Cvi-0, GCA_902460275.1GCA_902460275.1_Arabidopsis_thaliana_Cvi-0/
Eri-1, GCA_902460315.1GCA_902460315.1_Arabidopsis_thaliana_Eri-1/
Kyo, GCA_902460305.1GCA_902460305.1_Arabidopsis_thaliana_Kyo/
Sha, GCA_902460295.1GCA_902460295.1_Arabidopsis_thaliana_Sha/

Aligning a pair and running SyRI

SyRI reads a whole-genome alignment of two chromosome-level assemblies whose homologous chromosomes share a name, which the script arranges. For each pair, the commands are:

# asm5 is the preset for genomes of one species
# --eqx writes = and X in the CIGAR, which SyRI reads the mismatches from
minimap2 -cx asm5 --eqx Col-0.fa Ler.fa >Col-0_Ler.aln.paf

# -F P says the alignment is PAF
# --nc runs that many chromosomes at once
syri -c Col-0_Ler.aln.paf -r Col-0.fa -q Ler.fa -F P --prefix Col-0_Ler. --nc 5

In Col-0_Ler.syri.out, the structural regions are the rows with no parent: SYN, INV, TRANS, INVTR, DUP and INVDP.

SyRI regions as one PAF

A SyRI region is an interval on each of two genomes, the same shape as a PAF alignment record. syri_to_paf.py writes each region as one:

  • Sequence names are <genome>#1#<chrom>, so records from many pairs can share a file.
  • Inverted types go on the minus strand.
  • Two tags hold the type (syri) and the color plotsr gives that type (color).
  • Sequence lengths come from a .chrom.sizes file beside syri.out, the first two columns of the FASTA index.

Concatenate the records from every pair into one file, which every view below uses:

curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/syri_to_paf.py
for name in Col-0 Ler; do
  samtools faidx $name.fa
  cut -f1,2 $name.fa.fai >$name.chrom.sizes
done
python3 syri_to_paf.py Col-0_Ler.syri.out --reference Col-0 --query Ler
cat Col-0_*.paf Ler_Cvi.paf Cvi_Eri.paf Eri_Kyo.paf Kyo_Sha.paf >syri_pangenome.paf

The ribbons need no sequence, so each accession gets an assembly with a ChromSizesAdapter over its .chrom.sizes. Col-0 is one; Ler, Cvi, Eri, Kyo and Sha repeat it with their names and files:

Goes in the assemblies array of config.json. See Assemblies.

{
  "name": "Col-0",
  "uri": "Col-0.chrom.sizes"
}
jbrowse add-assembly Col-0.chrom.sizes \
  --name Col-0 \
  --load copy

In JBrowse Desktop, Open new genome on the start screen (or File → Open genome... in a session), then Open from a URL and paste:

Col-0.chrom.sizes

JBrowse reads the format off the file name. Then fill in:

  • Genome name: Col-0

Col-0.chrom.sizes is relative to a config.json. Replace it with its URL or its path on this computer.

Two entries in the track config matter here:

  • attributeColumns lists the PAF tags the palette button offers: syri becomes a color-by mode, and color is the color the file puts beside each type
  • the MultiWaySyntenyDisplay entry sets up the lanes view: rows.sort orders the lanes, and ribbons.encoding.color is a color scale on the bands, mapping the syri field through a scale.domain of the six types

Goes in the tracks array of config.json. See Tracks.

{
  "type": "SyntenyTrack",
  "trackId": "syri_pangenome",
  "name": "SyRI regions",
  "assemblyNames": ["Col-0", "Ler", "Cvi", "Eri", "Kyo", "Sha"],
  "adapter": {
    "type": "MultiGenomePAFAdapter",
    "uri": "syri_pangenome.paf",
    "attributeColumns": ["syri", "color"]
  },
  "displays": [
    {
      "type": "MultiWaySyntenyDisplay",
      "rows": { "sort": ["Ler", "Cvi", "Eri", "Kyo", "Sha"] },
      "ribbons": {
        "encoding": {
          "color": {
            "field": "syri",
            "scale": {
              "domain": ["SYN", "INV", "TRANS", "INVTR", "DUP", "INVDP"]
            }
          }
        }
      }
    }
  ]
}
jbrowse add-track-json '{
  "type": "SyntenyTrack",
  "trackId": "syri_pangenome",
  "name": "SyRI regions",
  "assemblyNames": ["Col-0", "Ler", "Cvi", "Eri", "Kyo", "Sha"],
  "adapter": {
    "type": "MultiGenomePAFAdapter",
    "uri": "syri_pangenome.paf",
    "attributeColumns": ["syri", "color"]
  },
  "displays": [
    {
      "type": "MultiWaySyntenyDisplay",
      "rows": { "sort": ["Ler", "Cvi", "Eri", "Kyo", "Sha"] },
      "ribbons": {
        "encoding": {
          "color": {
            "field": "syri",
            "scale": {
              "domain": ["SYN", "INV", "TRANS", "INVTR", "DUP", "INVDP"]
            }
          }
        }
      }
    }
  ]
}'

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": "syri_pangenome",
  "name": "SyRI regions",
  "assemblyNames": ["Col-0", "Ler", "Cvi", "Eri", "Kyo", "Sha"],
  "adapter": {
    "type": "MultiGenomePAFAdapter",
    "uri": "syri_pangenome.paf",
    "attributeColumns": ["syri", "color"]
  },
  "displays": [
    {
      "type": "MultiWaySyntenyDisplay",
      "rows": { "sort": ["Ler", "Cvi", "Eri", "Kyo", "Sha"] },
      "ribbons": {
        "encoding": {
          "color": {
            "field": "syri",
            "scale": {
              "domain": ["SYN", "INV", "TRANS", "INVTR", "DUP", "INVDP"]
            }
          }
        }
      }
    }
  ]
}

syri_pangenome.paf is relative to a config.json. Replace it with its URL or its path on this computer.

That shows it in the linear view. For the synteny view, open Add → Linear synteny view, pick the track under Quick start, and click Launch.

Columbia against Landsberg on chromosome 4

Open the first 6 Mb of chromosome 4 in both accessions and pick syri under Color by value on the palette button in the view header:

Goes at the top level of config.json, replacing any defaultSession there. See Default session.

{
  "defaultSession": {
    "name": "Col-0 vs Ler, chromosome 4",
    "views": [
      {
        "type": "LinearSyntenyView",
        "views": [
          { "assembly": "Col-0", "loc": "Chr4:1-6,000,000" },
          { "assembly": "Ler", "loc": "Chr4:1-6,000,000" }
        ],
        "tracks": [["syri_pangenome"]],
        "encoding": {
          "color": {
            "field": "syri",
            "scale": {
              "domain": ["SYN", "INV", "TRANS", "INVTR", "DUP", "INVDP"]
            }
          },
          "opacity": 0.9
        },
        "mark": { "interpolate": "bump" },
        "render": { "antialias": false },
        "collapseEmptyRows": true,
        "levelHeights": [260]
      }
    ]
  }
}
jbrowse set-default-session --session - << 'EOF'
{
  "name": "Col-0 vs Ler, chromosome 4",
  "views": [
    {
      "type": "LinearSyntenyView",
      "views": [
        { "assembly": "Col-0", "loc": "Chr4:1-6,000,000" },
        { "assembly": "Ler", "loc": "Chr4:1-6,000,000" }
      ],
      "tracks": [["syri_pangenome"]],
      "encoding": {
        "color": {
          "field": "syri",
          "scale": {
            "domain": ["SYN", "INV", "TRANS", "INVTR", "DUP", "INVDP"]
          }
        },
        "opacity": 0.9
      },
      "mark": { "interpolate": "bump" },
      "render": { "antialias": false },
      "collapseEmptyRows": true,
      "levelHeights": [260]
    }
  ]
}
EOF

Open this session in JBrowse Web ↗

The thin ribbons leaving the frame are duplications and translocations whose other end sits on another chromosome, which the label at the edge of the frame names. The key has one row per color, so INVTR shares a row with TRANS and INVDP with DUP.

Chromosome 4 in Col-0 above and Ler below, SyRI regions colored by type. The crossed ribbon is the inversion.
Open in JBrowse Web ↗

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

Or rebuild it from your own data:

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 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. For JBrowse Web, run jbrowse add-assembly once for each to put them in your config.json.This figure's rows, top to bottom: Col-0, Ler.
  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.A synteny track the session already has is quicker: pick it under Quick start, which fills in the rows itself.This figure uses “SyRI regions”.
  4. Click Launch.
  5. Synteny view header → palette button → Color by value → syriThe palette button's tooltip reads "Color by: ...".
  6. Synteny display settings (the sliders button in the view header) → Opacity → drag to 0.9Lower values let dense overlapping ribbons show through each other.
  7. Synteny display settings (the sliders button in the view header) → Curved lines (checked)
  8. Drag the bar below a synteny level to resize it.This figure's level is 260px tall.
  9. Row 1 (Col-0)
    1. Type your region of interest into the location box and press Enter.This figure is at Chr4:1-6,000,000.
  10. Row 2 (Ler)
    1. Type your region of interest into the location box and press Enter.This figure is at Chr4:1-6,000,000.

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

This session spec draws the figure. It goes after &session=spec- on a JBrowse Web link that loads https://jbrowse.org/code/jb2/main/test_data/syri/config.json, which is what the Web button above opens.

{
  "views": [
    {
      "type": "LinearSyntenyView",
      "views": [
        {
          "assembly": "Col-0",
          "loc": "Chr4:1-6,000,000"
        },
        {
          "assembly": "Ler",
          "loc": "Chr4:1-6,000,000"
        }
      ],
      "tracks": [
        [
          "syri_pangenome"
        ]
      ],
      "encoding": {
        "color": {
          "field": "syri",
          "scale": {
            "domain": [
              "SYN",
              "INV",
              "TRANS",
              "INVTR",
              "DUP",
              "INVDP"
            ]
          }
        },
        "opacity": 0.9
      },
      "mark": {
        "interpolate": "bump"
      },
      "render": {
        "antialias": false
      },
      "collapseEmptyRows": true,
      "levelHeights": [
        260
      ]
    }
  ]
}

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

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/code/jb2/main/test_data/syri/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearSyntenyView",
            "views": [
                {
                    "assembly": "Col-0",
                    "loc": "Chr4:1-6,000,000"
                },
                {
                    "assembly": "Ler",
                    "loc": "Chr4:1-6,000,000"
                }
            ],
            "tracks": [
                [
                    "syri_pangenome"
                ]
            ],
            "encoding": {
                "color": {
                    "field": "syri",
                    "scale": {
                        "domain": [
                            "SYN",
                            "INV",
                            "TRANS",
                            "INVTR",
                            "DUP",
                            "INVDP"
                        ]
                    }
                },
                "opacity": 0.9
            },
            "mark": {
                "interpolate": "bump"
            },
            "render": {
                "antialias": False
            },
            "collapseEmptyRows": True,
            "levelHeights": [
                260
            ]
        }
    ],
)
app  # display the widget

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file: a data file opens as the track its name says.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearSyntenyView",
      "views": [
        {
          "assembly": "Col-0",
          "loc": "Chr4:1-6,000,000"
        },
        {
          "assembly": "Ler",
          "loc": "Chr4:1-6,000,000"
        }
      ],
      "tracks": [
        [
          "syri_pangenome"
        ]
      ],
      "encoding": {
        "color": {
          "field": "syri",
          "scale": {
            "domain": [
              "SYN",
              "INV",
              "TRANS",
              "INVTR",
              "DUP",
              "INVDP"
            ]
          }
        },
        "opacity": 0.9
      },
      "mark": {
        "interpolate": "bump"
      },
      "render": {
        "antialias": false
      },
      "collapseEmptyRows": true,
      "levelHeights": [
        260
      ]
    }
  ]
}
JSON

npx @jbrowse/img synteny --config https://jbrowse.org/code/jb2/main/test_data/syri/config.json \
  --spec session.json \
  --width 1500 --out figure.svg

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

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

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearSyntenyView",
      "views": [
        {
          "assembly": "Col-0",
          "loc": "Chr4:1-6,000,000"
        },
        {
          "assembly": "Ler",
          "loc": "Chr4:1-6,000,000"
        }
      ],
      "tracks": [
        [
          "syri_pangenome"
        ]
      ],
      "encoding": {
        "color": {
          "field": "syri",
          "scale": {
            "domain": [
              "SYN",
              "INV",
              "TRANS",
              "INVTR",
              "DUP",
              "INVDP"
            ]
          }
        },
        "opacity": 0.9
      },
      "mark": {
        "interpolate": "bump"
      },
      "render": {
        "antialias": false
      },
      "collapseEmptyRows": true,
      "levelHeights": [
        260
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/syri/config.json \
  --width 1500 --height 460 \
  --timeout 120000 \
  --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.

Stacking the accessions, one SyRI run per band

The syri_pangenome track stacks all of them, each band drawing the SyRI run between the two genomes it joins:

Goes at the top level of config.json, replacing any defaultSession there. See Default session.

{
  "defaultSession": {
    "name": "Six Arabidopsis accessions, SyRI regions",
    "views": [
      {
        "type": "LinearSyntenyView",
        "views": [
          { "assembly": "Col-0" },
          { "assembly": "Ler" },
          { "assembly": "Cvi" },
          { "assembly": "Eri" },
          { "assembly": "Kyo" },
          { "assembly": "Sha" }
        ],
        "tracks": ["syri_pangenome"],
        "encoding": {
          "color": {
            "field": "syri",
            "scale": {
              "domain": ["SYN", "INV", "TRANS", "INVTR", "DUP", "INVDP"]
            }
          },
          "opacity": 0.9
        },
        "mark": { "interpolate": "bump" },
        "render": { "antialias": false },
        "collapseEmptyRows": true,
        "levelHeights": [150, 150, 150, 150, 150]
      }
    ]
  }
}
jbrowse set-default-session --session - << 'EOF'
{
  "name": "Six Arabidopsis accessions, SyRI regions",
  "views": [
    {
      "type": "LinearSyntenyView",
      "views": [
        { "assembly": "Col-0" },
        { "assembly": "Ler" },
        { "assembly": "Cvi" },
        { "assembly": "Eri" },
        { "assembly": "Kyo" },
        { "assembly": "Sha" }
      ],
      "tracks": ["syri_pangenome"],
      "encoding": {
        "color": {
          "field": "syri",
          "scale": {
            "domain": ["SYN", "INV", "TRANS", "INVTR", "DUP", "INVDP"]
          }
        },
        "opacity": 0.9
      },
      "mark": { "interpolate": "bump" },
      "render": { "antialias": false },
      "collapseEmptyRows": true,
      "levelHeights": [150, 150, 150, 150, 150]
    }
  ]
}
EOF

Open this session in JBrowse Web ↗

Arabidopsis accessions stacked, each band the SyRI comparison of the two genomes it joins.
Open in JBrowse Web ↗

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

Or rebuild it from your own data:

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 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. For JBrowse Web, run jbrowse add-assembly once for each to put them in your config.json.This figure's rows, top to bottom: Col-0, Ler, Cvi, Eri, Kyo, Sha.
  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.A synteny track the session already has is quicker: pick it under Quick start, which fills in the rows itself.This figure uses “SyRI regions”.
  4. Click Launch.
  5. Synteny view header → palette button → Color by value → syriThe palette button's tooltip reads "Color by: ...".
  6. Synteny display settings (the sliders button in the view header) → Opacity → drag to 0.9Lower values let dense overlapping ribbons show through each other.
  7. Synteny display settings (the sliders button in the view header) → Curved lines (checked)
  8. Drag the bar below a synteny level to resize it.This figure's 5 levels are 150, 150, 150, 150, 150px tall.

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

This session spec draws the figure. It goes after &session=spec- on a JBrowse Web link that loads https://jbrowse.org/code/jb2/main/test_data/syri/config.json, which is what the Web button above opens.

{
  "views": [
    {
      "type": "LinearSyntenyView",
      "views": [
        {
          "assembly": "Col-0"
        },
        {
          "assembly": "Ler"
        },
        {
          "assembly": "Cvi"
        },
        {
          "assembly": "Eri"
        },
        {
          "assembly": "Kyo"
        },
        {
          "assembly": "Sha"
        }
      ],
      "tracks": [
        "syri_pangenome"
      ],
      "encoding": {
        "color": {
          "field": "syri",
          "scale": {
            "domain": [
              "SYN",
              "INV",
              "TRANS",
              "INVTR",
              "DUP",
              "INVDP"
            ]
          }
        },
        "opacity": 0.9
      },
      "mark": {
        "interpolate": "bump"
      },
      "render": {
        "antialias": false
      },
      "collapseEmptyRows": true,
      "levelHeights": [
        150,
        150,
        150,
        150,
        150
      ]
    }
  ]
}

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

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/code/jb2/main/test_data/syri/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearSyntenyView",
            "views": [
                {
                    "assembly": "Col-0"
                },
                {
                    "assembly": "Ler"
                },
                {
                    "assembly": "Cvi"
                },
                {
                    "assembly": "Eri"
                },
                {
                    "assembly": "Kyo"
                },
                {
                    "assembly": "Sha"
                }
            ],
            "tracks": [
                "syri_pangenome"
            ],
            "encoding": {
                "color": {
                    "field": "syri",
                    "scale": {
                        "domain": [
                            "SYN",
                            "INV",
                            "TRANS",
                            "INVTR",
                            "DUP",
                            "INVDP"
                        ]
                    }
                },
                "opacity": 0.9
            },
            "mark": {
                "interpolate": "bump"
            },
            "render": {
                "antialias": False
            },
            "collapseEmptyRows": True,
            "levelHeights": [
                150,
                150,
                150,
                150,
                150
            ]
        }
    ],
)
app  # display the widget

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file: a data file opens as the track its name says.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearSyntenyView",
      "views": [
        {
          "assembly": "Col-0"
        },
        {
          "assembly": "Ler"
        },
        {
          "assembly": "Cvi"
        },
        {
          "assembly": "Eri"
        },
        {
          "assembly": "Kyo"
        },
        {
          "assembly": "Sha"
        }
      ],
      "tracks": [
        "syri_pangenome"
      ],
      "encoding": {
        "color": {
          "field": "syri",
          "scale": {
            "domain": [
              "SYN",
              "INV",
              "TRANS",
              "INVTR",
              "DUP",
              "INVDP"
            ]
          }
        },
        "opacity": 0.9
      },
      "mark": {
        "interpolate": "bump"
      },
      "render": {
        "antialias": false
      },
      "collapseEmptyRows": true,
      "levelHeights": [
        150,
        150,
        150,
        150,
        150
      ]
    }
  ]
}
JSON

npx @jbrowse/img synteny --config https://jbrowse.org/code/jb2/main/test_data/syri/config.json \
  --spec session.json \
  --width 1500 --out figure.svg

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

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

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearSyntenyView",
      "views": [
        {
          "assembly": "Col-0"
        },
        {
          "assembly": "Ler"
        },
        {
          "assembly": "Cvi"
        },
        {
          "assembly": "Eri"
        },
        {
          "assembly": "Kyo"
        },
        {
          "assembly": "Sha"
        }
      ],
      "tracks": [
        "syri_pangenome"
      ],
      "encoding": {
        "color": {
          "field": "syri",
          "scale": {
            "domain": [
              "SYN",
              "INV",
              "TRANS",
              "INVTR",
              "DUP",
              "INVDP"
            ]
          }
        },
        "opacity": 0.9
      },
      "mark": {
        "interpolate": "bump"
      },
      "render": {
        "antialias": false
      },
      "collapseEmptyRows": true,
      "levelHeights": [
        150,
        150,
        150,
        150,
        150
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/syri/config.json \
  --width 1500 --height 1040 \
  --timeout 120000 \
  --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.

Every accession in Columbia coordinates

To compare every accession with Col-0 in Col-0 coordinates, syri_to_paf.py also writes each pair's regions in reference coordinates, one BED row per region. Each row's name is its type, its color comes from itemRgb, and a query column holds the accession name. The rows against Col-0 concatenate into one track:

{
  head -n1 Col-0_Ler.regions.bed
  for name in Ler Cvi Eri Kyo Sha; do
    tail -n +2 Col-0_$name.regions.bed
  done | sort -k1,1 -k2,2n
} | bgzip >syri_regions.bed.gz
tabix -p bed syri_regions.bed.gz

In grammar-of-graphics terms, rows assigns one row per value of a field, here query, the accession, and rows.sort orders them:

Goes in the tracks array of config.json. See Tracks.

{
  "type": "FeatureTrack",
  "trackId": "syri_regions_on_Col-0",
  "name": "SyRI regions on Col-0, by accession",
  "assemblyNames": ["Col-0"],
  "adapter": {
    "type": "BedTabixAdapter",
    "uri": "syri_regions.bed.gz",
    "disableGeneHeuristic": true
  },
  "displays": [
    {
      "type": "LinearMultiRowFeatureDisplay",
      "rows": {
        "field": "query",
        "sort": ["Ler", "Cvi", "Eri", "Kyo", "Sha"]
      },
      "encoding": {
        "color": {
          "scale": {
            "domain": ["SYN", "INV", "TRANS", "INVTR", "DUP", "INVDP"]
          }
        }
      }
    }
  ]
}
jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "syri_regions_on_Col-0",
  "name": "SyRI regions on Col-0, by accession",
  "assemblyNames": ["Col-0"],
  "adapter": {
    "type": "BedTabixAdapter",
    "uri": "syri_regions.bed.gz",
    "disableGeneHeuristic": true
  },
  "displays": [
    {
      "type": "LinearMultiRowFeatureDisplay",
      "rows": {
        "field": "query",
        "sort": ["Ler", "Cvi", "Eri", "Kyo", "Sha"]
      },
      "encoding": {
        "color": {
          "scale": {
            "domain": ["SYN", "INV", "TRANS", "INVTR", "DUP", "INVDP"]
          }
        }
      }
    }
  ]
}'

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": "FeatureTrack",
  "trackId": "syri_regions_on_Col-0",
  "name": "SyRI regions on Col-0, by accession",
  "assemblyNames": ["Col-0"],
  "adapter": {
    "type": "BedTabixAdapter",
    "uri": "syri_regions.bed.gz",
    "disableGeneHeuristic": true
  },
  "displays": [
    {
      "type": "LinearMultiRowFeatureDisplay",
      "rows": {
        "field": "query",
        "sort": ["Ler", "Cvi", "Eri", "Kyo", "Sha"]
      },
      "encoding": {
        "color": {
          "scale": {
            "domain": ["SYN", "INV", "TRANS", "INVTR", "DUP", "INVDP"]
          }
        }
      }
    }
  ]
}

syri_regions.bed.gz is relative to a config.json. Replace it with its URL or its path on this computer.

We'll open a linear genome view on Col-0 at Chr4:1-6,000,000. Then:

  • Turn on SyRI regions on Col-0, by accession and SyRI regions.
  • Switch SyRI regions to Display types → Multi-way synteny display, which takes its lanes and colors from the track's MultiWaySyntenyDisplay entry.

Each accession is a lane, drawn in its assembly's coordinates and placed by the SyRI run against Col-0. The band between two lanes comes from the run between those two accessions, so it has the type SyRI gave that pair.

Goes at the top level of config.json, replacing any defaultSession there. See Default session.

{
  "defaultSession": {
    "name": "Six accessions in Col-0's coordinates",
    "views": [
      {
        "type": "LinearGenomeView",
        "assembly": "Col-0",
        "loc": "Chr4:1-6,000,000",
        "tracks": [
          {
            "trackId": "syri_regions_on_Col-0",
            "type": "LinearMultiRowFeatureDisplay",
            "height": 110
          },
          {
            "trackId": "syri_pangenome",
            "type": "MultiWaySyntenyDisplay",
            "height": 640
          }
        ]
      }
    ]
  }
}
jbrowse set-default-session --session - << 'EOF'
{
  "name": "Six accessions in Col-0's coordinates",
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "Col-0",
      "loc": "Chr4:1-6,000,000",
      "tracks": [
        {
          "trackId": "syri_regions_on_Col-0",
          "type": "LinearMultiRowFeatureDisplay",
          "height": 110
        },
        {
          "trackId": "syri_pangenome",
          "type": "MultiWaySyntenyDisplay",
          "height": 640
        }
      ]
    }
  ]
}
EOF

Open this session in JBrowse Web ↗

Col-0 chromosome 4 with a row of SyRI regions per accession above, and the accessions as lanes below.
Open in JBrowse Web ↗

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

Or rebuild it from your own data:

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 Col-0.
  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 BED (.bed.gz + .tbi).This figure uses “SyRI regions on Col-0, by accession”.
  3. Add the next track the same way.This figure uses “SyRI regions”.
  4. Type your region of interest into the location box and press Enter.This figure is at Chr4:1-6,000,000.

This session spec draws the figure. It goes after &session=spec- on a JBrowse Web link that loads https://jbrowse.org/code/jb2/main/test_data/syri/config.json, which is what the Web button above opens.

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "Col-0",
      "loc": "Chr4:1-6,000,000",
      "tracks": [
        {
          "trackId": "syri_regions_on_Col-0",
          "height": 110
        },
        {
          "trackId": "syri_pangenome",
          "height": 640
        }
      ]
    }
  ]
}

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

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/code/jb2/main/test_data/syri/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "Col-0",
            "loc": "Chr4:1-6,000,000",
            "tracks": [
                {
                    "trackId": "syri_regions_on_Col-0",
                    "height": 110
                },
                {
                    "trackId": "syri_pangenome",
                    "height": 640
                }
            ]
        }
    ],
)
app  # display the widget

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file: a data file opens as the track its name says.

npx @jbrowse/img --config https://jbrowse.org/code/jb2/main/test_data/syri/config.json \
  --assembly Col-0 --loc Chr4:1-6,000,000 \
  --track syri_regions_on_Col-0 '{"height":110}' \
  --track syri_pangenome '{"height":640}' \
  --width 1500 --out figure.svg

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

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

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "Col-0",
      "loc": "Chr4:1-6,000,000",
      "tracks": [
        {
          "trackId": "syri_regions_on_Col-0",
          "height": 110
        },
        {
          "trackId": "syri_pangenome",
          "height": 640
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/syri/config.json \
  --width 1500 --height 1000 \
  --timeout 120000 \
  --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.

Structural forms on the Arabidopsis pangenome page

The Arabidopsis pangenome page has SyRI regions for the 1001 Genomes Plus accessions on TAIR10. Type a gene or region there, and the page draws a map of that window with one row per structural form, a group of accessions with the same alleles at every structural-variant site in the window, beside its share of the accessions. The forms come from calling each accession against the pangenome graph with minigraph --call.

Two links on the page open the SyRI rows in JBrowse:

  • Open in JBrowse, under the map, opens the window as the graph with a row of SyRI regions per accession beneath it, the display that Every accession in Columbia coordinates sets up
  • Every accession as SyRI lanes, under the page title, opens the same rows over the chromosome 4 inversion

Reproduce it end to end

The script needs the tools under Prerequisites and works in four steps:

  1. Fetch the assemblies and keep the nuclear chromosomes, named Chr1 to Chr5, since SyRI pairs chromosomes by name.
  2. Align each accession to Col-0 and to the accession above it, and run SyRI on each alignment.
  3. Convert each SyRI table to PAF records and reference-coordinate BED rows.
  4. Write the config with the assemblies, the stacked track and the Col-0 regions track.
curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/build_syri_synteny.sh
bash build_syri_synteny.sh

For genomes of your own, pass a rows file after the output directory:

  • one <name> [accession] line per genome, in stack order, the reference first
  • the script uses a chromosome-level <name>.fa in the output directory as it is, so a row that has one needs no accession
  • homologous chromosomes must be spelled alike in every FASTA, since SyRI pairs them by name
bash build_syri_synteny.sh my_syri rows.txt

See also

Citations