thehardwarestore.ai

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tseemann/abricate ★ 512 104 APPLICATION

Abricate is a command-line tool for screening assembled genomic sequences (contigs) for antimicrobial resistance (AMR) genes and virulence factors. It uses BLAST+ to compare input sequences against a set of local databases (including NCBI AMRFinderPlus, CARD, Resfinder, ARG-ANNOT, MEGARES, EcOH, PlasmidFinder, VFDB, VICTORS, BacMet, and UPEC/ExPEC VF) and reports hits with detailed information such as gene identity, coverage, and associated resistance phenotype. The tool supports batch processing via file lists and can generate a presence/absence matrix across multiple samples. It is designed for genomic epidemiology workflows and is available via Bioconda or source installation.

RATING: 9.0/10 MAINT: active DRIFT: low
#amr-screening #virulence-genes #genomic-epidemiology #blast-tool #database-management #bioinformatics #command-line-tool #antimicrobial-resistance-genes #contigs #bioinformatics-tool #genomic-regions
▸ 1 reusable components found
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