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Bioinformatics. 2013 Jan 15;29(2):275-6. doi: 10.1093/bioinformatics/bts673. Epub 2012 Nov 19.

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

Author information

1
Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK. zam@well.ox.ac.uk

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 of a graph of known sequence and variation in a species, against which new samples can be compared rapidly. We demonstrate the ease-of-use and power by reproducing the results of studies using both long and short reads.

AVAILABILITY:

http://cortexassembler.sourceforge.net (GPLv3 license).

CONTACT:

zam@well.ox.ac.uk, mcvean@well.ox.ac.uk

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
23172865
PMCID:
PMC3546798
DOI:
10.1093/bioinformatics/bts673
[Indexed for MEDLINE]
Free PMC Article

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