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The HPRC pangenome on genomes.jbrowse.org

TL;DR: genomes.jbrowse.org's HPRC page draws the human pangenome graph on any GRCh38 region you type, beside a linear view of the same window, and a row of chromosome buttons draws each whole chromosome off a bubble tier. Nothing is built by hand; the HPRC pangenome tutorial is where the files come from.

Experimental

The graph view is a beta plugin, and the page is on staging.genomes.jbrowse.org until JBrowse 5 ships, because the plugin needs a build newer than the released hosts. We welcome your feedback.

Prerequisites

  • nothing to install: this is a click-path through a hosted page and the sessions it launches
  • to build the graph indexes yourself, or to add the same tracks to your own JBrowse, take the HPRC pangenome tutorial instead; every launch below opens a config it describes

Where the data comes from

The page launches one hosted config, https://jbrowse.org/pangenome/hprc-grch38/config.json, whose tracks are tabix projections of the release 2 sv.gfa and the release's own variant callset:

The HPRC page on genomes.jbrowse.org. Draw the MHC as a graph opens the graph on the class II window; the Explorer button goes to the locus catalog; Browse the pangenome on GRCh38 opens the reference-projected callset instead.

Two ways in

The HPRC page is for when you have a region: its Draw the graph form takes a GRCh38 locstring, and its chromosome row opens a whole chromosome at bubble resolution. The rest of this page walks that route.

The variable loci explorer is for when you have a gene: a catalog of GRCh38 loci where structure varies between haplotypes, each card carrying the same graph launch beside the variant summaries and genotype matrix for that locus.

The HPRC page's Draw the graph section: a region box preloaded with the MHC class II window, the catalog loci as presets, an Open in PangyPlot link for the same coordinates, and one button per chromosome.

Drawing a window

Open the HPRC page and scroll to Draw the graph. The box holds chr6:32,510,001-32,600,000, the MHC class II window, and the presets beneath it are catalog loci that minigraph draws well. Loci it collapses onto a single path (SMN1/2, RHD/RHCE, CYP2D6) are left out, because the graph there is a bare thread.

Type any region and press Draw as a graph. The note under the box says what the launch will cut. Past 150 kb it warns, because the layout scales to fit and a megabase-wide window draws as one thread; past 5 Mb, the view's own limit, it refuses.

The session is two panels. Above, a linear view with the RefSeq genes, the bubbles lane, the rGFA segments colored by rank (reference blue, everything else orange) and the allele inventory. Below, the graph, colored along the reference from red at the window's start to magenta at its end, with a segment that has no reference coordinate in charcoal. Hovering a node highlights its segment in the lane above, and the reverse.

The MHC class II window drawn from the page: RefSeq genes, bubbles, rank-colored segments and the allele inventory above, and the same window as a force-directed graph below, on the reference-position ramp.

Inside the session, the segments track's menu carries Launch → Graph genome view (this region), and rubberbanding a span offers Graph genome view (this selection), so a zoomed-in window reopens as a graph without the page. The graph reaches back the same way: hovering a node bands its interval across the lanes above, right-clicking one offers Highlight in hg38 and Open in hg38, and the view's own Launch menu reopens the whole window as a linear view. The HPRC tutorial lists every crossing and what each cannot do.

Drawing a whole chromosome

The chromosome row draws the tier the HPRC tutorial builds with build_bubble_tier.sh: one node per top-level bubble, so a whole chromosome is a few hundred nodes. The linear view above it swaps the segment-level lanes for the tier's own lane and a curve of segments per bubble.

chr21 whole, off the bubble tier: RefSeq genes, the variability curve and the tier lane above, and the tier as a graph below in the anchored layout, so the reference backbone runs under the same axis with each bubble's alternative hanging beneath it. 130 nodes for 46.7 Mb.

The chromosome launch opens in the Anchored layout, where every x is a reference coordinate, so the chain stays under the linear view it came from instead of bending into an arc. The Layout dropdown switches to force-directed.

The launch raises the view's maxRegionBp to the chromosome's length, since the 5 Mb default is a proxy for node count that a tier breaks. maxGraphNodes, the real ceiling, is unchanged.

Beyond 5 Mb at segment resolution

The graph view lays a window out in the browser, which caps it. For the same region at every scale, the form's Open in PangyPlot link opens PangyPlot, which precomputes an odgi layout and level-of-detail tiers server-side and navigates by the same chrom:start-end. It serves the release 1.1 graph, so a locus can differ in detail from the release 2 launch; both are on GRCh38, so the coordinates line up.

Adding the same tracks to your own instance

Every launch opens https://jbrowse.org/pangenome/hprc-grch38/config.json, a plain JBrowse config. The HPRC pangenome tutorial walks each of its tracks, and the session-spec URLs the page builds can be written by hand: a LinearGenomeView with an id, and a GraphGenomeView carrying loadedTrackId, loadedRegion and connectedViewId naming that id.