ABRicate
Description
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.
System 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