openpathogen is a free, open-source platform that screens FASTQ reads for antimicrobial resistance (AMR) and virulence genes using the KMA aligner compiled to WebAssembly. It runs entirely in your own browser and does not need any installation or account creation, and your sequence data never leaves your computer!

Choose input type

Forward reads (R1)

No file

Reverse reads (R2)

No file

Or fetch a public run

Quality control

Run fastp before alignment

Trims adapters and filters low-quality reads before alignment. Recommended.

Databases

ResFinder 2.6.0acquired resistance genes CARD 4.0.1protein homolog model VFDB set Acore virulence factors

Each selected database is screened against the reads in turn with KMA. Use the ↓ button to preload an index ahead of time — it is then cached in your browser.

Min identity 90%

Min coverage 60%