abricate

name	abricate
description	ABRicate — mass screening of contigs for AMR/virulence/plasmid markers against bundled databases (ResFinder, CARD, NCBI, VFDB, PlasmidFinder, EcoLI_VF, ARG-ANNOT, MEGARES, …). Use for fast multi-DB isolate or MAG screens and database concordance checks. Upstream: https://github.com/tseemann/abricate. Route via cge-finders / microbial-mining; official CGE CLI still via resfinder/plasmidfinder when phenotype mapping or PointFinder is required.
license	MIT
category	analysis-tools
tags	["ABRicate","AMR","virulence","PlasmidFinder","ResFinder","CARD","VFDB","screening"]
upstream	https://github.com/tseemann/abricate
stage	mining

ABRicate

Upstream: tseemann/abricate

Citation

Seemann, T. ABRicate: mass screening of contigs for antimicrobial and virulence genes. https://github.com/tseemann/abricate

Also cite the database papers for each --db used (ResFinder, CARD, PlasmidFinder, VFDB, … — see resfinder, rgi, plasmidfinder, virulencefinder).

See also docs/references.md and cge-finders.

Analytical thinking

ABRicate is a BLASTN mass-screen wrapper over multiple curated gene DBs. Ideal for: (1) quick multi-DB presence/absence, (2) cross-checking ResFinder vs CARD vs NCBI AMRFinder-style sets, (3) plasmid replicon + virulence gene panels on many assemblies.

Does not replace PointFinder chromosomal SNPs, ResFinder phenotype summaries, or CARD protein models (rgi). Thresholds (%ID / coverage) drive sensitivity — pin them in Methods. Metagenome contigs: expect fragmented hits.

How to run

mamba install -c bioconda -c conda-forge abricate
abricate --list                    # available DBs
abricate --db resfinder assembly.fasta > resfinder.tsv
abricate --db plasmidfinder assembly.fasta > plasmidfinder.tsv
abricate --db vfdb assembly.fasta > vfdb.tsv
abricate --summary *.tsv > summary.tsv
# update DBs periodically: abricate --setupdb / upstream instructions

Decision tree

Multi-DB gene screen on assemblies?
├─ Fast concordance / batch TSV → abricate
├─ CGE ResFinder + phenotype / PointFinder → resfinder (± pointfinder)
├─ CGE DisinFinder → disinfinder via resfinder
├─ CARD protein models → rgi
├─ Official PlasmidFinder CLI → plasmidfinder
└─ Plasmid ST schemes → pmlst

Related skills

cge-finders · resfinder · plasmidfinder · disinfinder · virulencefinder · staramr · rgi · pmlst · mlst · microbial-mining · tool-selection