ABRicate

Description

abricate website

Mass screening of contigs for antimicrobial resistance or virulence genes. It comes bundled with multiple databases: NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and VFDB.

Environment Modules

Run module spider abricate to find out what environment modules are available for this application.

Environment Variables

• HPC_ABRICATE_DIR - installation directory
• HPC_ABRICATE_BIN - executable directory

Citation

If you publish the results of Abricate please cite both the software and the appropriate database you used with --db

Seemann T, Abricate, Github https://github.com/tseemann/abricate

NCBI AMRFinderPlus - doi: 10.1128/AAC.00483-19

CARD - doi:10.1093/nar/gkw1004

Resfinder - doi:10.1093/jac/dks261

ARG-ANNOT - doi:10.1128/AAC.01310-13

VFDB - doi:10.1093/nar/gkv1239

PlasmidFinder - doi:10.1128/AAC.02412-14

EcOH - doi:10.1099/mgen.0.000064

MEGARES 2.00 - doi:10.1093/nar/gkz1010

Categories

phylogenetics