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ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

View ORCID ProfileMartin Hunt, Alison E. Mather, View ORCID ProfileLeonor Sánchez-Busó, View ORCID ProfileAndrew J. Page, View ORCID ProfileJulian Parkhill, Jacqueline A. Keane, View ORCID ProfileSimon R. Harris
doi: https://doi.org/10.1101/118000
Martin Hunt
1Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK, CB10 1SA
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Alison E. Mather
1Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK, CB10 1SA
2Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK, CB3 0ES
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Leonor Sánchez-Busó
1Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK, CB10 1SA
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Andrew J. Page
1Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK, CB10 1SA
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Julian Parkhill
1Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK, CB10 1SA
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Jacqueline A. Keane
1Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK, CB10 1SA
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Simon R. Harris
1Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK, CB10 1SA
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  • ORCID record for 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 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.

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Posted April 07, 2017.
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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
bioRxiv 118000; doi: https://doi.org/10.1101/118000
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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
bioRxiv 118000; doi: https://doi.org/10.1101/118000

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