High-throughput microbial population genomics using the Cortex variation assembler.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 23172865.
- Also identified by DOI 10.1093/bioinformatics/bts673 and PMC identifier 3546798.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
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. http://cortexassembler.sourceforge.net (GPLv3 license). zam@well.ox.ac.uk, mcvean@well.ox.ac.uk Supplementary data are available at Bioinformatics online.
Medical subject headings
- Genetic Variation
- Metagenomics
- Software