Synteny visualization (all-vs-all minimap2)

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.13. Desktop beta builds are coming soon.

Strains of one bacterial species share most of their chromosome and differ by gene islands one strain picked up and by stretches that flipped. We align five E. coli strains against each other with minimap2, stack them in a linear synteny view, and read where they differ: Sakai's Shiga-toxin prophage, the phenylacetate (paa) operon three strains lack, and IAI39's inversions.

We'll start by aligning the five strains with minimap2 -X, which writes one all-vs-all PAF, an alignment of every genome against every other. Then we:

load the PAF with MultiGenomePAFAdapter and stack the five assemblies as rows
add a gene track per strain, and read one strain against the rest in a single pileup

The alternative to one all-vs-all file is a separate alignment for each pair of adjacent rows, which Synteny visualization (pairwise minimap2) follows through three H. pylori strains. Pairwise files need no renaming, and suit a few genomes in a fixed order.

Prerequisites

a JBrowse to open the files in: Desktop takes a local file by path, Web through Add track
the NCBI datasets CLI
minimap2
samtools
htslib (bgzip, tabix)
unzip
node, for the JBrowse CLI

Where the data comes from

Show full URLs

Five E. coli RefSeq assemblies, each fetched by accession with the datasets CLI.

The build script takes these files from their URLs, so there is nothing to download by hand.

Producing an all-vs-all PAF

minimap2 aligning PanSN-named genomes against themselves writes an all-vs-all PAF, as does the mapping step of PGGB, the PanGenome Graph Builder. PanSN names every sequence sample#haplotype#contig, e.g. K12#1#chr.

The script reduces each assembly to one chr record. The JBrowse assemblies use the strain FASTAs as they are; only the concatenated copy minimap2 aligns has PanSN names, with haplotype 1 throughout:

for strain in K12 Sakai CFT073 NCTC86 IAI39; do
  # '>chr' -> '>K12#1#chr'
  awk -v s="$strain" '/^>/{print ">" s "#1#chr"; next} {print}' "$strain.fa"
done > all.fa

# -c: emit the base-level CIGAR the linear synteny view needs
# -X: skip self-alignments and the reciprocal half of every pair
minimap2 -c -x asm20 -X all.fa all.fa > all_vs_all.paf

Setting up the five assemblies

Each strain FASTA becomes an assembly whose name matches an entry in assemblyNames on the track:

for strain in K12 Sakai CFT073 NCTC86 IAI39; do
  bgzip -f "$strain.fa"
  samtools faidx "$strain.fa.gz"   # writes the .fai and .gzi JBrowse needs
  jbrowse add-assembly "$strain.fa.gz" --name "$strain" --load copy
done

The same step for one strain, as a config or in Desktop:

Config file

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

{
  "name": "K12",
  "uri": "K12.fa.gz"
}

CLI (add-assembly)

jbrowse add-assembly K12.fa.gz \
  --name K12 \
  --load copy

JBrowse Desktop

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

K12.fa.gz
K12.fa.gz.fai
K12.fa.gz.gzi

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

Genome name: K12

K12.fa.gz is relative to a config.json. Replace it with its URL or its path on this computer.

An assembly whose refNames still have the PanSN prefix draws empty. The assemblies configuration guide has more.

Loading the PAF with MultiGenomePAFAdapter

List every assembly the file covers in assemblyNames; the adapter keeps only the records whose PanSN prefixes match the pair of rows each band joins:

Config file

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

{
  "type": "SyntenyTrack",
  "trackId": "ecoli_ava",
  "name": "E. coli pangenome (all-vs-all PAF)",
  "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"],
  "adapter": {
    "type": "MultiGenomePAFAdapter",
    "uri": "all_vs_all.paf",
    "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"]
  }
}

CLI (add-track)

jbrowse add-track all_vs_all.paf \
  --trackId ecoli_ava \
  --name "E. coli pangenome (all-vs-all PAF)" \
  --assemblyNames K12,Sakai,CFT073,NCTC86,IAI39 \
  --adapterType MultiGenomePAFAdapter \
  --load copy

In the app

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": "ecoli_ava",
  "name": "E. coli pangenome (all-vs-all PAF)",
  "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"],
  "adapter": {
    "type": "MultiGenomePAFAdapter",
    "uri": "all_vs_all.paf",
    "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"]
  }
}

all_vs_all.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.

The config names MultiGenomePAFAdapter because a .paf extension makes JBrowse guess the pairwise PAFAdapter, which reads two assembly names. An assembly name that differs from its PanSN sample prefix needs a map.¹

Large files: index with make-pif

MultiGenomePAFAdapter reads the whole PAF into memory. For many samples, index it with jbrowse make-pif and switch to MultiGenomeIndexedPAFAdapter, fetching only the region in view:

# produces all_vs_all.pif.gz and all_vs_all.pif.gz.tbi
jbrowse make-pif all_vs_all.paf

make-pif prints the add-track command for the samples it found:

jbrowse add-track all_vs_all.pif.gz --adapterType MultiGenomeIndexedPAFAdapter \
  -a CFT073,IAI39,K12,NCTC86,Sakai --load copy

Only the adapter block differs from the un-indexed version:

Config file

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

{
  "type": "SyntenyTrack",
  "trackId": "ecoli_ava_indexed",
  "name": "E. coli all-vs-all (indexed)",
  "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"],
  "adapter": {
    "type": "MultiGenomeIndexedPAFAdapter",
    "uri": "all_vs_all.pif.gz",
    "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"]
  }
}

CLI (add-track)

jbrowse add-track all_vs_all.pif.gz \
  --trackId ecoli_ava_indexed \
  --name "E. coli all-vs-all (indexed)" \
  --assemblyNames K12,Sakai,CFT073,NCTC86,IAI39 \
  --adapterType MultiGenomeIndexedPAFAdapter \
  --load copy

In the app

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": "ecoli_ava_indexed",
  "name": "E. coli all-vs-all (indexed)",
  "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"],
  "adapter": {
    "type": "MultiGenomeIndexedPAFAdapter",
    "uri": "all_vs_all.pif.gz",
    "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"]
  }
}

all_vs_all.pif.gz 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.

make-pif also writes a coarse copy of the alignments for zoomed-out views.²

Stacking the five strains

Stacking the strains from the import form

Add → Linear synteny view opens the form in Quick start.
Choose ecoli_ava, whose five assemblies become rows.
Click Launch.

Manual mode builds the stack by hand: Add row per strain, and the connector button between each pair to pick its track.

The all-vs-all Quick start in the import form. The ecoli_ava track fills its five assemblies in as rows, and Launch opens the stack.

Stacking the strains in a defaultSession

A defaultSession holding a LinearSyntenyView opens the stack on load:

Config file

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

{
  "defaultSession": {
    "name": "E. coli 5-strain pangenome",
    "views": [
      {
        "type": "LinearSyntenyView",
        "views": [
          { "assembly": "K12" },
          { "assembly": "Sakai" },
          { "assembly": "CFT073" },
          { "assembly": "NCTC86" },
          { "assembly": "IAI39" }
        ],
        "tracks": ["ecoli_ava"],
        "minAlignmentLength": 10000,
        "collapseEmptyRows": true
      }
    ]
  }
}

CLI (set-default-session)

jbrowse set-default-session --session - << 'EOF'
{
  "name": "E. coli 5-strain pangenome",
  "views": [
    {
      "type": "LinearSyntenyView",
      "views": [
        { "assembly": "K12" },
        { "assembly": "Sakai" },
        { "assembly": "CFT073" },
        { "assembly": "NCTC86" },
        { "assembly": "IAI39" }
      ],
      "tracks": ["ecoli_ava"],
      "minAlignmentLength": 10000,
      "collapseEmptyRows": true
    }
  ]
}
EOF

Open in JBrowse

Open this session in JBrowse Web ↗

tracks names the track once, and the view puts it on every band whose two rows its assemblyNames cover
collapseEmptyRows gives each trackless row a bare scale bar

Row order is a free choice with an all-vs-all PAF, since the file aligns every pair.

Five E. coli strains stacked from one minimap2 all-vs-all PAF, short alignments hidden with minAlignmentLength. The continuous ribbons are the backbone shared by all five; the bottom band crosses because IAI39 has inversions against the others.

Adding gene tracks to see what a gap holds

Each strain's GFF becomes a gene track attached to that strain's assembly:

for strain in K12 Sakai CFT073 NCTC86 IAI39; do
  jbrowse sort-gff "$strain.gff" | bgzip > "$strain.gff.gz"
  tabix "$strain.gff.gz"
  # -a "$strain": attach the track to that one assembly, so it stays with that row
  jbrowse add-track "$strain.gff.gz" -a "$strain" --name "$strain genes" --load copy
done

Navigate the K-12 row to chr:1,026,000-1,126,000 and the Sakai row to chr:1,205,000-1,305,000. The gap right of the ribbon holds stx2A and stx2B, the Shiga-toxin subunits, with no alignment to K-12.

K-12 (top) and Sakai (bottom) with their gene tracks, framing the Sp5 prophage. The synteny ribbon runs out at the shared-backbone boundary, and stx2B sits in the stretch past it with no counterpart in K-12.

One strain against all the others

In a plain linear genome view, where no second row names a target assembly, the ecoli_ava track draws the viewed strain against every other strain in the file. Clicking an alignment can launch a synteny view against its mate, the strain it aligns to.

Group by... in the track menu is a facet: it splits the track into stacked sections, one per value of a field. Three track-menu items set the pileup up for reading strain by strain:

Group by... → Mate assembly gives each strain a section. Untick Show... → Collapse groups to one row to stack every section, or expand one from its label.
Group by... → Hide self-alignment lane drops the section for the strain you're viewing. The figures below have it ticked.
Show... → Show coverage adds a histogram of how many other strains cover each base.

The figure below shows K-12's phenylacetate (paa) operon, where three strains stop at the shaded edge and NCTC86 runs through, with a track of the pangenome graph's segments, built with minigraph in the E. coli pangenome tutorial, above the sections.

Above, one track with one section per strain: K-12 against every other sample in the file, grouped by mate assembly. Below, the same window as a graph, where the short arm beside the ringed node is the detour the other three take.

At whole-chromosome zoom, the same sections also fit on the K-12 row of the five-strain stack:

List IAI39 second in the session's views.
Add ecoli_ava to the K-12 row from that row's track selector.
Pick Strand from the palette button, so an inversion is blue in both halves.

The one-vs-all sections on the K-12 row of the five-strain stack, both drawn from the same PAF and colored by strand. White gaps are where a strain has no alignment to the K-12 backbone. IAI39 sits directly below K-12, so its blue stretches and the blue crossings under them are the same inversions.

Percent identity per strain

Display types → Marks in the track menu draws each ecoli_ava alignment as a line at its identity, one row per strain, with nothing to configure. The plot is the percent identity plot PipMaker drew for a pair of genomes. In grammar-of-graphics terms, the config below writes it out: rows assigns one row per mate.assemblyName, filter drops records, scales.y is the y scale, and the mark is the shape drawn. Three details to read:

identity comes from minimap2's de divergence tag
filter drops K-12's alignments to itself, which otherwise take a row of their own
scales.y.zero is false, so the autoscaled axis spans the identities alone

Advanced → Edit plot... in the same menu shows these keys as text and applies edits live.

Config file

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

{
  "type": "SyntenyTrack",
  "trackId": "ecoli_ava_identity",
  "name": "K-12 against each strain, identity",
  "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"],
  "adapter": {
    "type": "MultiGenomePAFAdapter",
    "uri": "https://jbrowse.org/demos/ecoli_pangenome/all_vs_all.paf.gz",
    "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"]
  },
  "displays": [
    {
      "type": "LinearMarkDisplay",
      "displayId": "ecoli_ava_identity-LinearMarkDisplay",
      "rows": "mate.assemblyName",
      "filter": ["jexl:feature.mate.assemblyName != 'K12'"],
      "scales": { "y": { "zero": false } },
      "marks": [{ "mark": "rule", "encoding": { "y": "identity", "size": 2 } }]
    }
  ]
}

CLI (add-track-json)

jbrowse add-track-json '{
  "type": "SyntenyTrack",
  "trackId": "ecoli_ava_identity",
  "name": "K-12 against each strain, identity",
  "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"],
  "adapter": {
    "type": "MultiGenomePAFAdapter",
    "uri": "https://jbrowse.org/demos/ecoli_pangenome/all_vs_all.paf.gz",
    "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"]
  },
  "displays": [
    {
      "type": "LinearMarkDisplay",
      "displayId": "ecoli_ava_identity-LinearMarkDisplay",
      "rows": "mate.assemblyName",
      "filter": ["jexl:feature.mate.assemblyName != '\''K12'\''"],
      "scales": { "y": { "zero": false } },
      "marks": [{ "mark": "rule", "encoding": { "y": "identity", "size": 2 } }]
    }
  ]
}'

In the app

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": "ecoli_ava_identity",
  "name": "K-12 against each strain, identity",
  "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"],
  "adapter": {
    "type": "MultiGenomePAFAdapter",
    "uri": "https://jbrowse.org/demos/ecoli_pangenome/all_vs_all.paf.gz",
    "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"]
  },
  "displays": [
    {
      "type": "LinearMarkDisplay",
      "displayId": "ecoli_ava_identity-LinearMarkDisplay",
      "rows": "mate.assemblyName",
      "filter": ["jexl:feature.mate.assemblyName != 'K12'"],
      "scales": { "y": { "zero": false } },
      "marks": [{ "mark": "rule", "encoding": { "y": "identity", "size": 2 } }]
    }
  ]
}

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.

Open in JBrowse

Open this track in JBrowse Web ↗

Open this track in JBrowse Desktop ↗ (JBrowse Desktop 5.0+)

K-12 against each other strain, one row per strain, each alignment a line at its identity. NCTC86 runs closest to K-12, and the short, less similar alignments fall at the same places in every row.

Redrawing each lane in its own strain's coordinates

A strain with no alignment to the backbone is a white gap on the K-12 axis. Display types → Multi-way synteny display redraws each lane in the coordinates of the strain it shows, one ribbon per PAF record. The ortholog-table tutorial has a figure of the display.

Launching a stacked view at one locus

Drag-select a region on the scale bar and pick Launch → Linear synteny view. The dialog lists every assembly aligning to that region as a panel, top to bottom, with arrows to reorder them and a checkbox to drop one; Replace current view or Open in new view launches the stack. Ribbons draw between neighbouring rows only.

Right-clicking a single alignment offers three routes under Launch:

Linear synteny view with Sakai (or whichever strain the alignment names) opens that one pair.
Linear synteny view, all assemblies here opens the same multi-strain dialog.
Open Sakai at the matching region opens a linear genome view of Sakai at that region.

Right-clicking one alignment in the one-vs-all lanes: the pair it describes, every strain aligning here, or a linear view of that strain, in one Launch submenu.

A rubberband selection over the shared backbone, the Launch → Linear synteny view entry it raises, the dialog listing a panel per strain, and the five-row stack it opens.

From the lanes to the stack for one locus: a scale-bar selection raises Launch, the dialog lists a panel per strain that aligns to the window, and its arrows move IAI39 up under K-12 before the launch replaces the lane view with the stack.

Video

Open the session the video starts in ↗, then take the steps it shows:

K-12, with one alignment lane per other strain
Select the locus on the scale bar and launch a synteny view
Ribbons join neighbouring rows only, so the order picks the pairs
Move IAI39 up to sit under K-12
IAI39 under K-12: each white wedge is sequence only one of them has

Steps

Open this view in JBrowse Web ↗ · Open this view in JBrowse Desktop ↗

Desktop link does nothing?

It needs JBrowse Desktop 5.0+. Or 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%2Fecoli_pangenome%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22K12%22%2C%22loc%22%3A%22chr%3A795%2C000-815%2C000%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22ecoli_ava%22%2C%22type%22%3A%22LGVSyntenyDisplay%22%2C%22facet%22%3A%22mateAssembly%22%2C%22hideSelfAlignments%22%3Atrue%2C%22featureHeight%22%3A14%2C%22height%22%3A135%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+synteny%2Fallvsall_launch_from_selection

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:

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 K12, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
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 figure uses “E. coli pangenome (all-vs-all PAF)”.
1. Track menu → Group by... → Mate assemblySynteny tracks only: one section per assembly on the other side of the alignment.
2. Track menu → Group by... → Hide self-alignment lane (checked)Below a divider at the foot of that submenu, and only meaningful on an all-vs-all track, which is what has a self lane.
3. Track menu → Feature height → Custom... → 14px
Type your region of interest into the location box and press Enter.This figure is at chr:795,000-815,000.

Spec

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

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:795,000-815,000",
      "tracks": [
        {
          "trackId": "ecoli_ava",
          "type": "LGVSyntenyDisplay",
          "facet": "mateAssembly",
          "hideSelfAlignments": true,
          "featureHeight": 14,
          "height": 135
        }
      ]
    }
  ]
}

Notebook

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/demos/ecoli_pangenome/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "K12",
            "loc": "chr:795,000-815,000",
            "tracks": [
                {
                    "trackId": "ecoli_ava",
                    "type": "LGVSyntenyDisplay",
                    "facet": "mateAssembly",
                    "hideSelfAlignments": True,
                    "featureHeight": 14,
                    "height": 135
                }
            ]
        }
    ],
)
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 with --bam, --vcfgz and the other file flags.

npx @jbrowse/img --config https://jbrowse.org/demos/ecoli_pangenome/config.json \
  --assembly K12 --loc chr:795,000-815,000 \
  --track ecoli_ava display:LGVSyntenyDisplay '{"facet":"mateAssembly","hideSelfAlignments":true,"featureHeight":14,"height":135}' \
  --width 1920 --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.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "K12",
      "loc": "chr:795,000-815,000",
      "tracks": [
        {
          "trackId": "ecoli_ava",
          "type": "LGVSyntenyDisplay",
          "facet": "mateAssembly",
          "hideSelfAlignments": true,
          "featureHeight": 14,
          "height": 135
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/ecoli_pangenome/config.json \
  --width 1920 --height 640 \
  --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.

A launched view is a few kilobases wide, so it draws each indel from the CIGAR minimap2 -c wrote. CIGAR indels in the settings menu sets them to colored, transparent or none.

Checking the Sakai gap against the PAF

To print the alignments between two strains near a gap, here Sakai against K-12 at the stx2 island, set s and m to the two strain prefixes and lo and hi to the window. Because -X emits each pair once in either direction, the coordinates come from whichever column the strain landed in:

awk -F'\t' -v OFS='\t' -v s=Sakai -v m=K12 '
  $1 ~ "^" s "#" && $6 ~ "^" m "#" { print $3, $4; next }
  $1 ~ "^" m "#" && $6 ~ "^" s "#" { print $8, $9 }
' all_vs_all.paf | sort -n | awk -v lo=1200000 -v hi=1300000 '$1 < hi && $2 > lo'

1207288	1207877
1210882	1246166
1251954	1252260
1274685	1275548

The second line is the shared backbone the ribbon draws. The third is short, and the fourth starts at 1,274,685, so stx2A and stx2B fall in a stretch with no K-12 counterpart.

Reproduce it end to end

build_ecoli_pangenome_synteny.sh runs everything on this page, download and preparation included, and needs the tools under Prerequisites:

Download the five RefSeq assemblies with their annotation and keep each chromosome as chr, so the plasmids drop out and every row reads the same name.
Concatenate the strains under PanSN names and align them with minimap2 -X, so each pair is aligned once and no strain aligns to itself.
Rename each GFF's chromosome features to chr too, so the genes load on that strain's row.
Write the config with the five assemblies, the gene tracks, the all-vs-all track and the five-row session.

curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/build_ecoli_pangenome_synteny.sh
bash build_ecoli_pangenome_synteny.sh          # builds ./ecoli_pangenome_build/jbrowse2
npx --yes serve ecoli_pangenome_build/jbrowse2 # then open the printed URL

Notes

assemblyNameToPanSN maps such a name, e.g. { "Ecoli_K12": "K12" }. A haplotype-resolved pangenome can map each haplotype to a separate assembly with a sample#haplotype prefix; see PanSN depth. ↩
--coarse sets how many bp a coarse row may stray from the real alignment; with a larger value, raise coarseBpPerPxThreshold on the adapter too. --csi swaps the TBI index for sequences over ~512 Mb. ↩

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Synteny visualization (all-vs-all minimap2)

Prerequisites#

Where the data comes from#

Producing an all-vs-all PAF#

Setting up the five assemblies#

Loading the PAF with MultiGenomePAFAdapter#

Large files: index with make-pif#

Stacking the five strains#

Stacking the strains from the import form#

Stacking the strains in a defaultSession#

Adding gene tracks to see what a gap holds#

One strain against all the others#

Percent identity per strain#

Redrawing each lane in its own strain's coordinates#

Launching a stacked view at one locus#

Checking the Sakai gap against the PAF#

Reproduce it end to end#

See also#

Notes

Prerequisites

Where the data comes from

Producing an all-vs-all PAF

Setting up the five assemblies

Loading the PAF with MultiGenomePAFAdapter

Large files: index with make-pif

Stacking the five strains

Stacking the strains from the import form

Stacking the strains in a defaultSession

Adding gene tracks to see what a gap holds

One strain against all the others

Percent identity per strain

Redrawing each lane in its own strain's coordinates

Launching a stacked view at one locus

Checking the Sakai gap against the PAF

Reproduce it end to end

See also