Community-curated, species-specific quality control thresholds for bacterial de novo genome assemblies.
Website: https://qualibact.org
This repository is the Next.js website. It renders thresholds and per-species statistics produced upstream by qualibact-engine (which compares AllTheBacteria assemblies against NCBI RefSeq genomes, applies Isolation-Forest outlier filtering, and emits the FINAL/WARN bounds plus distribution stats).
Downstream, the published thresholds are consumed by SpecCheck — a CLI that flags assemblies that fall outside their species' QualiBact band.
https://qualibact.org/— the live site (Cloudflare Pages, custom domain).https://qualibact.org/api/v2/— public threshold API:thresholds.csv/.json/.xlsx,index.json,threshold-rationale.yml.https://qualibact.org/{Genus}/{Species}/{scheme}/— per-species page (thresholds, summary stats, PASS/WARN/FAIL ATB genome lists, refseq calibration set, distribution plots).https://qualibact.org/methods/qualibact-v1.0/— engine pipeline + percentile-band methodology.https://qualibact.org/methods/qualibact-v1.1/— expert-feedback overrides layered on top of v1.0.
qualibact-v1.0— raw engine output (no manual overrides). 307 species.qualibact-v1.1— expert-review layer on top of v1.0: pinned thresholds requested by domain experts, plus a small number of curated re-runs on different reference sets. 15 species (only species with an actual change ship a v1.1 row; everything else falls back to v1.0 automatically).REFSEQ-QC-v1— RefSeq-only baseline. 10 species.
- Next.js 16 (App Router, static export) + React 19 + TypeScript.
- Tailwind CSS 3 with
next-themes(light default). - MDX content in
content/. - Python ingest pipeline (
scripts/build_manifests.py). - Cloudflare Pages hosting; Cloudflare R2 for bulk static assets (PNGs, ATB tier CSVs, refseq archives, per-assembly stats).
npm install
npm run dev # http://localhost:3000
npm run build # static export to ./out/
npm run lint # ESLint
npm run build-manifests # rebuild per-(species, scheme) manifest.json + /api/v2/ aggregatesA full local build needs engine output staged under public/static/species/{Species}/{scheme}/. The committed tree ships only the build-time-required slice (manifest.json + summary.csv per pair, plus /api/v2/ and /static/summary/ aggregates); bulk plots / CSVs live on R2.
PRs welcome. Major contributions to source code, manuscript development, metric validation, or providing additional data for calibrating quality thresholds qualify for authorship on publications.
- Threshold revision requests for a specific species → file via the Requests page on the website or open an issue.
- New experts willing to review a species' thresholds — see the Contributors page; the survey + sign-off process is described there.
A QualiBact publication is in preparation. In the meantime, please link to https://qualibact.org and cite the relevant scheme version (e.g. qualibact-v1.0 or qualibact-v1.1) when referencing a specific bound.