openpathogen About

What is openpathogen, and how does it work?

Developed by Amulya Baral

openpathogen is an open-source, privacy-friendly, zero-install pathogen profiling platform.

It uses KMA (read-based gene detection), version 1.5.1, compiled to WebAssembly.

All of your data is analyzed locally in your own browser, and does not have to be uploaded to a server anywhere. This makes it fast, private, and safe to use even with sensitive clinical or unpublished sequencing data.

Because everything runs client-side, there is no account to create and no server that you have to put your trust on. The only network traffic is the one-time download of the WebAssembly engine and whichever reference database you select.

Databases are downloaded once and cached in your browser (IndexedDB), so repeat runs against the same database start instantly. The first run against a large database may take a moment while it downloads.

Getting started

  1. Choose your input type: paired-end, single-end, or Nanopore. In Advanced mode you also choose the reference database; Simple mode runs all of them.
  2. Select your read file(s) (.fastq or gzipped .fastq.gz), or load the example isolate — S. aureus USA300_TCH1516 (SRR10341524), a 48 MB MiSeq run of the community-associated MRSA reference strain, downloaded straight from ENA and cached in your browser. You should see mecA, blaZ plus aminoglycoside and macrolide genes on ResFinder, and PVL/hla on VFDB. You can also fetch any public run by its accession (SRR…, ERR…, DRR…) with Or fetch a public run; the organism and read type are detected automatically, and files are limited to 1 GB each.
  3. Start the analysis. Live progress is streamed into the Logs panel, which you can expand at any time to watch the KMA command and its output.

Databases for read-based gene detection

Right now, we support these databases:

ResFinder 2.6.0
Acquired AMR genes (CGE).
CARD 4.0.1
Comprehensive Antibiotic Resistance Database, protein homolog model.
VFDB
Virulence Factor Database Set A (core).

Some notes

  • Defaults of 80% identity and 80% coverage have been chosen following common reporting thresholds; this does not in any way mean they are absolute. For example, you can lower the identity threshold to recover divergent variants, or lower the coverage threshold for fragmented or low-depth samples.
  • Nanopore mode enables KMA's -bcNano for indel-aware base calling.
  • You can click any detected gene in the results to inspect its coverage, consensus sequence, alignment, and variants.
  • The output bundle includes .res, .aln, .fsa, .frag.gz, .mat.gz, .vcf.gz, and .mapstat.
  • openpathogen needs a modern browser with SharedArrayBuffer support (recent Chrome, Firefox, Edge, or Safari).

Citation

We have a short communication in preparation. Please cite KMA and the relevant database in the meantime:

Clausen PTLC, Aarestrup FM, Lund O. Rapid and precise alignment of raw reads against redundant databases with KMA. BMC Bioinformatics. 2018;19:307. doi:10.1186/s12859-018-2336-6