| 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
integron_finder genome.fna --outdir integron_out
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
