$ show tseemann/abricate
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.
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A standalone Perl script that automates the download, extraction, and formatting of antimicrobial resistance and virulence gene databases from various sources (HTTP, FTP, git) into BLAST+ compatible format. Demonstrates a robust pattern for maintaining bioinformatics databases with error handling, logging, and support for multiple source types.