RT Journal Article
SR Electronic
T1 ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 118000
DO 10.1101/118000
A1 Martin Hunt
A1 Alison E. Mather
A1 Leonor Sánchez-Busó
A1 Andrew J. Page
A1 Julian Parkhill
A1 Jacqueline A. Keane
A1 Simon R. Harris
YR 2017
UL http://biorxiv.org/content/early/2017/03/18/118000.abstract
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.