Genome Coverage Explorer

An interactive, zoomable view of vertebrate taxonomy that shows, clade by clade, how much has a reference genome — and how much of the gap remains. One of the Revive & Restore genome-gap demos: the exploratory, visual companion to the analytical reviverestore-genomegap search. Both are built independently on the same three Underlay collections.

What it shows

• A zoomable sunburst of vertebrate taxonomy (class → order → family). Each arc is sized by species count and coloured by the share with a reference genome — bright aqua is sequenced, dark is the gap.
• Click a wedge to dive into a clade, the centre to zoom back out, a family to list its species. Hover anything to inspect it.
• A side panel with the focused clade's coverage, species / sequenced / gap / threatened counts, and a per-child coverage breakdown.
• Deep-linkable: /?clade=Mammalia opens focused on a clade.

Data

Built at deploy time from three versioned, content-addressed Underlay collections, reconciled through the GBIF taxonomic backbone:

Collection	Role
reviverestore/iucn-species	conservation status + taxonomy (IUCN Red List, via GBIF)
reviverestore/ncbi-assemblies	genome assembly metadata (NCBI Datasets)
reviverestore/gbif-backbone	taxonomic reconciliation keys

scripts/build-data.ts fetches all three, joins on the GBIF backbone key, and writes public/data/tree.json (the aggregated class→order→family hierarchy that drives the sunburst) plus species.json (flat rows for the family drill-in) and meta.json.

Run locally

cp .env.example .env      # set UNDERLAY_API_KEY (read-scoped dev key)
pnpm install
pnpm prebuild             # fetch + join -> public/data/
pnpm dev                  # http://localhost:5173

public/data/ is gitignored; pnpm prebuild (and pnpm build) regenerate it.

Deploy

Cloudflare Pages, connected to this repo. Build command pnpm build, output directory dist/. Set UNDERLAY_API_URL, UNDERLAY_API_KEY, and VITE_UNDERLAY_URL in the Pages environment.

Live: demo-reviverestore-explorer.knowledgefutures.org (pending Pages setup).

Stack

Vite + React 19 + Tailwind 4 + TypeScript, per the KF demo conventions. The sunburst is d3-hierarchy (partition) + d3-shape (arc) with a requestAnimationFrame tween on zoom; colour interpolation via d3-scale / d3-interpolate.