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Journal article

High-throughput microbial population genomics using the Cortex variation assembler.

Abstract:

SUMMARY: We have developed a software package, Cortex, designed for the analysis of genetic variation by de novo assembly of multiple samples. This allows direct comparison of samples without using a reference genome as intermediate and incorporates discovery and genotyping of single-nucleotide polymorphisms, indels and larger events in a single framework. We introduce pipelines which simplify the analysis of microbial samples and increase discovery power; these also enable the construction o...

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Publication status:
Published
Peer review status:
Peer reviewed

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Publisher copy:
10.1093/bioinformatics/bts673

Authors


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Institution:
University of Oxford
Division:
MSD
Department:
NDM
Role:
Author
More by this author
Institution:
University of Oxford
Division:
MPLS
Department:
Statistics
Role:
Author
More by this author
Institution:
University of Oxford
Division:
MSD
Department:
NDM
Role:
Author
More from this funder
Funding agency for:
Mcvean, G
Grant:
WT086084/Z/08/Z
Publisher:
Oxford University Press Publisher's website
Journal:
Bioinformatics (Oxford, England) Journal website
Volume:
29
Issue:
2
Pages:
275-276
Publication date:
2013-01-01
DOI:
EISSN:
1367-4811
ISSN:
1367-4803
Source identifiers:
363824
Language:
English
Keywords:
Subjects:
UUID:
uuid:c7b57beb-3bb3-498b-af45-caca31f1b361
Local pid:
pubs:363824
Deposit date:
2013-11-17

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