TY - JOUR T1 - ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads JF - bioRxiv DO - 10.1101/118000 SP - 118000 AU - Martin Hunt AU - Alison E. Mather AU - Leonor Sánchez-Busó AU - Andrew J. Page AU - Julian Parkhill AU - Jacqueline A. Keane AU - Simon R. Harris Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/03/18/118000.abstract N2 - 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. ER -