PT - JOURNAL ARTICLE AU - Hunt, Martin AU - Mather, Alison E. AU - Sánchez-Busó, Leonor AU - Page, Andrew J. AU - Parkhill, Julian AU - Keane, Jacqueline A. AU - Harris, Simon R. TI - ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads AID - 10.1101/118000 DP - 2017 Jan 01 TA - bioRxiv PG - 118000 4099 - http://biorxiv.org/content/early/2017/04/07/118000.short 4100 - http://biorxiv.org/content/early/2017/04/07/118000.full AB - Antimicrobial resistance (AMR) is one of the major threats to human and animal health worldwide, yet few high-throughput tools exist to analyse and predict the resistance of a bacterial isolate from sequencing data. Here we present a new tool, ARIBA, that identifies AMR-associated genes and single nucleotide polymorphisms directly from short reads, and generates detailed and customisable output. The accuracy and advantages of ARIBA over other tools are demonstrated on three datasets from Gram-positive and Gram-negative bacteria, with ARIBA outperforming existing methods. ARIBA is available at https://github.com/sanger-pathogens/ariba.