AMR and virulence gene detection in the browser. Reads never leave your machine.
Open openpathogen.org, load FASTQ files (Illumina or Nanopore) or fetch a public run by accession, and run. No install, no account, no upload. Background, citations and usage notes are on the About page.
One click runs the pipeline: optional quality control with fastp (compiled to wasm64 WebAssembly from source; see fastp/WASM_BUILD.md), then read mapping with KMA against any combination of ResFinder, CARD and VFDB, with adjustable identity and coverage thresholds. The results open with a report: resistance genes grouped by drug class with the antibiotics they affect (from ResFinder's phenotype table), the drug classes with no acquired gene, and virulence factors by VFDB category. The report prints or saves as a PDF. Below it are a gene table per database with a viewer per gene (coverage, consensus, alignment, variants), the fastp reports, and a ZIP with the full KMA output.
All tools run locally as WebAssembly: a 64-bit (Memory64) build in Chrome, Edge and Firefox, and a 32-bit build of the same sources in Safari and on iPhone and iPad, where every browser uses Safari's engine and Memory64 is not available (kma/WASM_BUILD.md §3f, fastp/WASM_BUILD.md). Both give the same gene calls; the 32-bit build has at most 4 GB of memory, less on a phone. Databases download on first use, are checked against pinned SHA-256 hashes (js/integrity.js) and are cached in the browser.
Example isolate: S. aureus USA300_TCH1516 (SRR10341524), a 48 MB community-associated MRSA run downloaded from ENA and cached in your browser. Any other public run can be fetched by accession (SRR, ERR, DRR).
CABBAGE tested-resistance rates. When the species is known (filled in for public runs, or typed in), each resistance gene in the report also shows how often isolates of that species carrying it tested resistant in CABBAGE (Dickens et al., NAR 2026). CABBAGE links 170,750 sequenced isolates to 1.7 million susceptibility test results. For example, mecA reads "In CABBAGE, S. aureus with mecA tested resistant to methicillin in 97.7% of 1,792 isolates". Rates are shown only for antibiotics the gene is known to affect (listed by ResFinder, or linked to the gene by drug name in CABBAGE), and only from at least 20 tested isolates. They are exported as cabbage_predictions.csv in the results ZIP. The snapshot downloads once (under 1 MB) and is cached. To browse the full database use the EMBL-EBI AMR portal. The snapshot is rebuilt with scripts/fetch-cabbage.py and scripts/build-cabbage.py; scripts/pin-hashes.sh updates the hash pins after any database change.
Run locally: any static file server at the repo root works, for example python3 -m http.server 8000. The bundled service worker adds the cross-origin isolation headers that WebAssembly threads need and reloads the page once on first visit.