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TETyper: a bioinformatic pipeline for classifying variation and genetic contexts of transposable elements from short-read whole-genome sequencing data

Abstract:

Much of the worldwide dissemination of antibiotic resistance has been driven by resistance gene associations with mobile genetic elements (MGEs), such as plasmids and transposons. Although increasing, our understanding of resistance spread remains relatively limited, as methods for tracking mobile resistance genes through multiple species, strains and plasmids are lacking. We have developed a bioinformatic pipeline for tracking variation within, and mobility of, specific transposable elements...

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Publication status:
Published
Peer review status:
Peer reviewed
Version:
Publisher's Version

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Publisher copy:
10.1099/mgen.0.000232

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Institution:
University of Oxford
Division:
Medical Sciences Division
Department:
NDM
Subgroup:
NDM Experimental Medicine
More by this author
Institution:
University of Oxford
Division:
Medical Sciences Division
Department:
NDM
Subgroup:
NDM Experimental Medicine
German-Mesner, I More by this author
Vegesana, K More by this author
More by this author
Institution:
University of Oxford
Division:
Medical Sciences Division
Department:
NDM
Subgroup:
NDM Experimental Medicine
ORCID:
0000-0002-0412-8509
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National Institute for Health Research Health Protection Research Unit More from this funder
Public Health England More from this funder
University of Virginia More from this funder
More from this funder
Grant:
Broad Agency Announcement (BAA 2016-N-17812)
Publisher:
Microbiology Society Publisher's website
Journal:
Microbial Genomics Journal website
Volume:
4
Issue:
12
Publication date:
2018-11-22
Acceptance date:
2018-10-12
DOI:
EISSN:
2057-5858
Pubs id:
pubs:949119
URN:
uri:c575b6f8-8c6b-4306-90c4-bdec3c1e0b22
UUID:
uuid:c575b6f8-8c6b-4306-90c4-bdec3c1e0b22
Local pid:
pubs:949119

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