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2 graph genome (pangenome) view: rGFA reference-anchored layouts, the Bandage force-directed engine, and haplotype lanes read from a gbz-base database","maintainers":[{"name":"cmdcolin","email":"colin.diesh@gmail.com"}],"readme":"# jbrowse-plugin-graphgenomeviewer\n\nPangenome graphs in JBrowse 2.\n\n## As a track of a linear view\n\nA `GraphTrack` cuts the graph for the view's window and redraws it as you pan. A\nforce-directed track draws a strip of the reference segments at their bp above\nthe graph, each in its node's colour, so the graph reads against the tracks\nabove it.\n\n- **LPA's KIV-2 repeat.** The goldenrod outlines on the graph are the gene\n  track's LPA exons. The charcoal loops, sequence off the reference, hang inside\n  the array the curated VNTR track marks.\n\n![KIV-2 as a graph track under RefSeq genes and the curated KIV-2 annotation, its reference segments on a strip at their bp](img/force_kiv2.png)\n\n- **Each haplotype takes its own loops.** Side by side, one walk per panel:\n  HG01960 skips most of GRCh38's loops for the big one, and HG00133 takes both.\n\n![The KIV-2 array side by side: GRCh38, HG00097, HG01960 and HG00133 each followed start to end](img/force_kiv2_facet.png)\n\n- **Copy number off a bar.** Walk rows tile each haplotype by the 5,548 bp\n  kringle: GRCh38's six units are the six LPA exon pairs above, and HG00133\n  has 27.\n\n![KIV-2 walk rows under LPA and the curated KIV-2 annotation](img/walk_rows_kiv2.png)\n\n- **Variants at their bp.** A tube map on the reference axis puts each of MICB's\n  variant columns under its exon. HPRC's multiple alignment, cut to the same\n  eight haplotypes, marks a mismatch in a row wherever its tube leaves GRCh38's\n  route.\n\n![MICB's exons 2–4 as a tube map on the reference axis under the RefSeq genes and the eight haplotypes' alignment rows](img/tube_map_micb_ref.png)\n\n## As its own view\n\n**Add → Graph genome view** opens a whole GFA file. A graph track's **Launch →\nGraph genome view** opens the cut on screen, drawn as the track draws it; a\nsession spec does the same with `loadedTrackId` and `loadedRegion`. Hovering a\nnode in the view bands its bp in the linear view:\n\n![The MICB cut as a view under its linear view, a variant's box hovered and its bp banded in exon 2](img/tube_map_micb.png)\n\n## Features\n\n- Seven layouts: force-directed (Bandage FMMM), ordered, anchored, sample rows,\n  walk rows, and sequenceTubeMap's tube map on its own axis or the reference's\n- Genes from the session's annotation track, drawn on the graph\n- Hovering a callset or MAF row in the same view lifts that haplotype's walk\n- Bubbles from `gfatools bubble` or the graph itself, opened level by level\n- gbz-base haplotypes as walks: the number of walks through a node as its\n  thickness, walks lifted out as metro-map lanes or side by side, a panel per\n  walk or a row per sample, each shading from its start to its end\n- GAF reads in the tube map, with their mismatches, from a gbz-base track\n- Figures as SVG, from the view's Export SVG or from a JSON spec with no browser\n  ([docs/figures.md](docs/figures.md))\n\n## Usage\n\nNeeds JBrowse 5.0.0-beta.11 or later.\n\n```json\n{\n  \"plugins\": [\n    {\n      \"name\": \"GraphGenomeView\",\n      \"esmUrl\": \"https://jbrowse.org/plugins/jbrowse-plugin-graphgenomeviewer/latest/dist/jbrowse-plugin-graphgenomeviewer.esm.js\"\n    }\n  ]\n}\n```\n\n- **File → Open track** opens an rGFA index (`.segs.bed.gz` from\n  `build_rgfa_tabix.sh`) or a gbz-base database (`.gbz.db`) as a `GraphTrack`.\n  It finds the links and indexes beside the url, which a presigned url's\n  signature doesn't cover; spell out each location in a config instead\n- A hand-written track needs only the adapter:\n\n```json\n{\n  \"type\": \"GraphTrack\",\n  \"trackId\": \"hprc_graph\",\n  \"name\": \"HPRC release 2 graph\",\n  \"assemblyNames\": [\"hg38\"],\n  \"adapter\": {\n    \"type\": \"RgfaTabixAdapter\",\n    \"uri\": \"https://example.com/hprc\",\n    \"coarse\": {\n      \"uri\": \"https://example.com/hprc.tier10000\",\n      \"aboveBpPerPx\": 1000\n    }\n  }\n}\n```\n\n- The track menu picks layout, colour and walk, and switches to the segments\n  lane or, for gbz-base, the haplotype lanes\n- Cuts the window plus a window each side, up to 5 Mb; past `aboveBpPerPx`, the\n  `coarse` tier (`build_bubble_tier.sh` in jbrowse-components)\n- gbz-base past the cut (5 Mb, or the adapter's `nodeLimit`) draws the haplotype\n  index's overview instead: a band of how many haplotypes diverge from the\n  reference by 50 bp or more, then a row per haplotype, the track's lanes first.\n  Needs an index from `gbz-haplotype-index` 0.3 or later\n- gbz-base swaps in `{ \"type\": \"GbzBaseSyntenyAdapter\", \"uri\": \"….gbz.db\" }`; an\n  `hg38` or `hs1` track finds the graph's GRCh38 or CHM13 reference sample, and\n  `assemblyNameToPanSN` covers other names\n- `\"reads\": \"….gaf.gz\"` on that adapter draws GAF reads in the tube map layouts,\n  fetched through its tabix index; [docs/layouts.md](docs/layouts.md#reads) has\n  the config and how to make one\n\n## Docs\n\n- [docs/layouts.md](docs/layouts.md) — layouts, bubbles, walks, genes, loci\n- [docs/developing.md](docs/developing.md) — building, testing, `host-compat`\n\n## License\n\nGPL-3.0-or-later (this module is based on work from Bandage and ODGF graph\ndrawing algorithms which are both GPL).\n","readmeFilename":"README.md"}