integronfinder

name	integronfinder
description	IntegronFinder — detect integrons (intI, attC, cassettes) in bacterial genomes/assemblies, including AMR cassette context. Use for integron-focused MGE mining. Upstream: https://github.com/gem-pasteur/Integron_Finder. Route via microbial-mining; pair with rgi / mobileog / genomad.
license	MIT
category	analysis-tools
tags	["IntegronFinder","integron","MGE","AMR","cassette","genome-mining"]
upstream	https://github.com/gem-pasteur/Integron_Finder
stage	mining

IntegronFinder

Upstream: gem-pasteur/Integron_Finder

Citation

Néron, B. et al. IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella. Microorganisms 10, 700 (2022). https://doi.org/10.3390/microorganisms10040700

Original: Cury, J. et al. Identification and analysis of integrons and cassette arrays in bacterial genomes. Nucleic Acids Res. 44, 4539–4550 (2016). https://doi.org/10.1093/nar/gkw319

See also docs/references.md.

Analytical thinking

Integrons capture and express gene cassettes (often AMR). IntegronFinder locates complete/CALIN/In0-style architectures. Intersect cassette genes with rgi / deeparg for resistome context; do not equate integron presence with expression.

How to run

# bioconda / pip per upstream; example
integron_finder genome.fna --outdir integron_out
# optional functional annotation flags — follow IntegronFinder 2 docs

Decision tree

Integrons / cassettes?
├─ Yes → integronfinder
├─ IS elements → isescan
├─ MGE protein machinery → mobileog
├─ Plasmid/virus contigs → genomad
└─ ARG catalogue → rgi (± deeparg)

Related skills

rgi · deeparg · mobileog · isescan · genomad · microbial-mining · tool-selection