Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data

Will Rowe; Kate S. Baker; David Verner-Jeffreys; Craig Baker-Austin; Jim J. Ryan; Duncan Maskell; Gareth Pearce

doi:10.1371/journal.pone.0133492

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Open Access

Peer-reviewed

Research Article

Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data

Will Rowe ,

* E-mail: wpmr2@cam.ac.uk

Affiliation Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
⨯
Kate S. Baker,

Affiliation Wellcome Trust Sanger Institute, Cambridge, United Kingdom
⨯
David Verner-Jeffreys,

Affiliation Centre for Environment, Fisheries and Aquaculture Science, Weymouth, United Kingdom
⨯
Craig Baker-Austin,

Affiliation Centre for Environment, Fisheries and Aquaculture Science, Weymouth, United Kingdom
⨯
Jim J. Ryan,

Affiliation Environment, Health and Safety, GlaxoSmithKline, Ware, United Kingdom
⨯
Duncan Maskell,

Affiliation Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
⨯
Gareth Pearce

Affiliation Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
⨯

Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data

Will Rowe,
Kate S. Baker,
David Verner-Jeffreys,
Craig Baker-Austin,
Jim J. Ryan,
Duncan Maskell,
Gareth Pearce

Published: July 21, 2015
https://doi.org/10.1371/journal.pone.0133492

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Illumina BaseSpace App and Docker container image now available.

Posted by wpmr2 on 20 Dec 2015 at 20:58 GMT

SEAR is now available for use as an App on the BaseSpace platform (Illumina).
This iteration of SEAR has been updated, changes include:
- The use of the open source VSEARCH (instead of USEARCH).
- New result output.

Please try it at:
https://basespace.illumin...

Finally, the SEAR source code (for the App, Docker container image and original code) is available on GitHub:
https://github.com/wpmr2/...

Competing interests declared: Author of the manuscript.

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Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data

Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data

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Illumina BaseSpace App and Docker container image now available.

Posted by wpmr2 on 20 Dec 2015 at 20:58 GMT