| name | defensefinder |
| description | Detect anti-phage defense systems in prokaryotic genomes. Use this skill when working with defensefinder: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/mdmparis/defense-finder. For routing across mining tasks use microbial-mining. For stage order use metagenomics-workflow.
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| license | MIT |
| category | analysis-tools |
| tags | ["defense","CRISPR","genome-mining"] |
| upstream | https://github.com/mdmparis/defense-finder |
| stage | mining |
DefenseFinder
Upstream: DefenseFinder
Citation
Tesson, F. et al. Systematic and quantitative view of the antiviral arsenal of prokaryotes. Nat. Commun. 13, 2561 (2022). https://doi.org/10.1038/s41467-022-30269-9
See also docs/references.md.
Analytical thinking
Mines defense systems (CRISPR and beyond). Complements padloc (different
system models — often run both for surveys) and viral MGE mining
(genomad / virsorter2) for host–virus interaction stories.
How to run
conda install -c bioconda defense-finder
defense-finder run genome.faa --out temp/defense/${id}
Key parameters
| input | proteins preferred | From Bakta/Prokka |
| models | installed DB | Pin |
Decision notes
- Run mining on QC-filtered genomes/MAGs (or contigs for MGE/virus screens)
- Computational hits are hypotheses — state validation limits in Methods
- Pin software + database releases
Related skills
padloc · genomad · virsorter2 · spacedust · bakta · antismash ·
microbial-mining · tool-selection · metagenomics-workflow
