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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 - http://doi.org/10.1128/AAC.00483-19

CARD - http://doi.org/10.1093/nar/gkw1004

Resfinder - http://doi.org/10.1093/jac/dks261

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

VFDB - http://doi.org/10.1093/nar/gkv1239

PlasmidFinder - http://doi.org/10.1128/AAC.02412-14

EcOH - http://doi.org/10.1099/mgen.0.000064

MEGARES 2.00 - http://doi.org/10.1093/nar/gkz1010

Categories

phylogenetics