AMR Gene Species Filter — a browser-based tool that filters antimicrobial resistance (AMR) gene predictions by bacterial species. It is a TypeScript port of scagaire by Andrew Page, running entirely client-side with no server required.
When you run an AMR prediction tool (Abricate, StarAMR, RGI-CARD) on a genome, you may get many false positives — genes from commensal bacteria that are not relevant to your target species. ScagaireX filters these out by checking each predicted gene against a species-specific database of known AMR genes, removing those not known to occur in the target species.
| Format | Tool | File |
|---|---|---|
| Abricate | Abricate v0.9.7 / v0.9.8 | Any TSV output |
| StarAMR | StarAMR | resfinder.tsv |
| RGI-CARD | RGI | TSV output |
Format is auto-detected from the header line. You can also override it manually.
The species-gene database is sourced from scagaire's species_to_genes.tsv, which maps bacterial species to AMR genes observed across public databases.
All processing happens client-side in your browser. No data is uploaded to any server.
# Install dependencies
npm install
# Start dev server
npm run dev
# Run tests
npm test
# Build for production
npm run build# Build
docker build -t scagairex .
# Run
docker run -p 8080:80 scagairex
# Browse http://localhost:8080If you use ScagaireX in your research, please cite the original scagaire tool:
Page AJ. scagaire: species-aware AMR gene filtering. https://github.com/andrewjpage/scagaire
GPL-3.0-only
Nabil-Fareed Alikhan — Centre for Genomic Pathogen Surveillance, University of Oxford