Abricate: Mass Screening of Bacterial Genome Assemblies Against Curated Gene Sequence Databases

Abricate is a Unix command line bioinformatics tool for screening bacterial genome assemblies for the presence of specific DNA sequences, most commonly antibiotic resistance genes, virulence factors, and genotyping amplicons. Abricate accepts many input sequence formats, optionally compressed, and outputs machine readable tabular reports. Individual reports from different genomes can be combined into a tabular summary report in a presence/absence matrix format. The minimum percentage identity and coverage for a sequence to be reported can be set at runtime. Included are twelve popular databases, and users can create custom databases. Abricate is written in Perl 5 and is available under an open source GPL licence from github.com/tseemann/abricate.