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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
Version:
Publisher's version

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Publisher copy:
10.1093/bioinformatics/bts673

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Institution:
University of Oxford
Department:
Oxford, MSD, Clinical Medicine
Role:
Author
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Institution:
University of Oxford
Department:
Oxford, MPLS, Statistics
Role:
Author
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Institution:
University of Oxford
Department:
Oxford, MPLS, Statistics, Clinical Medicine
Role:
Author
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Funding agency for:
McVean, G
Publisher:
Oxford University Press Publisher's website
Journal:
Bioinformatics (Oxford, England) Journal website
Volume:
29
Issue:
2
Pages:
275-276
Publication date:
2013-01-05
DOI:
EISSN:
1367-4811
ISSN:
1367-4803
URN:
uuid:c7b57beb-3bb3-498b-af45-caca31f1b361
Source identifiers:
363824
Local pid:
pubs:363824

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