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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.ukSupplementary data are available at Bioinformatics online.

Original publication

DOI

10.1093/bioinformatics/bts673

Type

Journal article

Journal

Bioinformatics (Oxford, England)

Publication Date

01/2013

Volume

29

Pages

275 - 276

Addresses

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

Keywords

Genomics, Genotype, Polymorphism, Single Nucleotide, Software, INDEL Mutation, Genetic Variation, Metagenomics