| 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
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
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
