ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

Martin Hunt, Alison E Mather, Leonor Sánchez-busó, Andrew J Page, Julian Parkhill, Jacqueline A Keane, Simon R Harris

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Abstract

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 customizable 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.
Original languageEnglish
Article number000131
JournalMicrobial Genomics
Volume3
Issue number10
Early online date4 Sep 2017
DOIs
Publication statusPublished - 1 Oct 2017
Externally publishedYes

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