defensefinder

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.
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  # if packaged; else follow upstream docs

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