| name | virulencefinder |
| description | VirulenceFinder — CGE virulence gene detection in bacterial assemblies/reads for supported species (historically E. coli, Enterococcus, S. aureus, Listeria, …). Upstream: https://bitbucket.org/genomicepidemiology/virulencefinder / PyPI Virulencefinder. Route via cge-finders / microbial-mining; not a general metagenome pathogenicity score.
|
| license | MIT |
| category | analysis-tools |
| tags | ["VirulenceFinder","CGE","virulence","pathogen","isolate","typing"] |
| upstream | https://bitbucket.org/genomicepidemiology/virulencefinder |
| stage | mining |
VirulenceFinder
Upstream: virulencefinder ·
DB: virulencefinder_db ·
PyPI: Virulencefinder
Citation
Joensen, K. G. et al. Real-time whole-genome sequencing for routine typing,
surveillance, and outbreak detection of verotoxigenic Escherichia coli.
J. Clin. Microbiol. 52, 4214–4220 (2014).
https://doi.org/10.1128/JCM.02452-14
See also docs/references.md and cge-finders.
Analytical thinking
VirulenceFinder matches curated virulence markers for supported species
databases. Coverage is not pan-bacterial; check which species DB is selected.
Gene presence ≠ expression, toxin production, or clinical virulence.
For open metagenomes, treat hits cautiously (contamination / partial contigs).
Pair with taxonomy (gtdbtk / isolate ID) before strong pathogenicity claims.
AMR remains resfinder / rgi; plasmids plasmidfinder / genomad.
How to run
python -m virulencefinder -ifa assembly.fasta -o vf_out \
-db_path /path/to/virulencefinder_db
Pin tool + DB versions; report which species database was used.
Decision tree
Virulence markers?
├─ Supported CGE species DB → virulencefinder
├─ AMR genes → resfinder / rgi
├─ Plasmids → plasmidfinder / genomad
├─ Named MGEs → mobileelementfinder
└─ Unsure / environmental community → do not over-claim from VF hits alone
Related skills
cge-finders · resfinder · plasmidfinder · mobileelementfinder ·
staramr · rgi · genomad · microbial-mining · tool-selection
