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- Title
High-throughput microbial population genomics using the Cortex variation assembler.
- Authors
Iqbal, Zamin; Turner, Isaac; McVean, Gil
- 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.ukSupplementary information: Supplementary data are available at Bioinformatics online.
- Subjects
MICROBIAL population genetics; BIOLOGICAL variation; COMPUTER software; SINGLE nucleotide polymorphisms; PIPELINE computers; COMPARATIVE studies
- Publication
Bioinformatics, 2013, Vol 29, Issue 2, p275
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/bts673