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The HPRC pangenome on genomes.jbrowse.org

TL;DR: genomes.jbrowse.org's HPRC page launches the Minigraph-Cactus graph as a graph, on any GRCh38 region you type, beside a linear view of the same window. 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 the one to take when a region is what you have. Its Draw the graph form takes a GRCh38 locstring and opens the graph cut to that window, and its chromosome row opens a whole chromosome at bubble resolution. The rest of this page walks that route.

The variable loci explorer is the one to take when a gene is what you have. It is a catalog of GRCh38 loci where structure varies between haplotypes, and each locus card carries the same graph launch, sized to the window the graph draws well, beside the variant summaries and the 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 arrives holding chr6:32,510,001-32,600,000, the MHC class II window, and the presets beneath it are the catalog's loci that minigraph draws well; the ones it collapses onto a single path (SMN1/2, RHD/RHCE, CYP2D6) are left out on purpose, because the graph there is a bare thread and reads as an empty result.

Type any region, with or without commas, and press Draw as a graph. The note under the box says what the launch will cut. Past 150 kb it warns instead: the layout scales the graph to fit, so a megabase-wide window draws as one unreadable thread rather than as loops. The cut is refused outright past 5 Mb, which is the view's own limit.

The session that opens is two panels. Above, a linear view of the window with the RefSeq genes, the bubbles lane, the rGFA segments colored by rank (reference blue, everything else orange) and the allele inventory, which draws each insertion at its real magnitude. 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 hovering the lane highlights the node.

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.

The form is only the first cut. 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 going back to the page.

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 chr1's 249 Mb is a few hundred nodes and lays out in milliseconds. The linear view above it swaps the segment-level lanes for the tier's own lane and a curve of segments per bubble, which is where the graph varies and by how much.

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, rather than the force-directed default: a few hundred nodes in a chain bend into an arc under a force layout, and anchored keeps them under the linear view they came from. The Layout dropdown switches between the two.

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

Beyond 5 Mb at segment resolution

The graph view cuts a window and lays it out in the browser, which is what makes it self-hosting and what caps it. For the same region at every scale in between, 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. Its instance serves the release 1.1 graph, so a locus can differ in detail from the release 2 launch beside it; the coordinates line up because both are on GRCh38.

Adding the same tracks to your own instance

Every launch above opens https://jbrowse.org/pangenome/hprc-grch38/config.json, which is a plain JBrowse config you can read. The HPRC pangenome tutorial walks each of its tracks, from the plugin declaration through the rGFA indexes to the tier, and the same 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.