PT  - JOURNAL ARTICLE
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
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/2017/03/18/118000.short
4100  - http://biorxiv.org/content/early/2017/03/18/118000.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.