{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T00:35:53Z","timestamp":1774312553255,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1413,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/cortexassembler.sourceforge.net (GPLv3 license).<\/jats:p>\n               <jats:p>Contact: \u00a0zam@well.ox.ac.uk, mcvean@well.ox.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts673","type":"journal-article","created":{"date-parts":[[2012,11,21]],"date-time":"2012-11-21T01:49:46Z","timestamp":1353462586000},"page":"275-276","source":"Crossref","is-referenced-by-count":44,"title":["High-throughput microbial population genomics using the Cortex variation assembler"],"prefix":"10.1093","volume":"29","author":[{"given":"Zamin","family":"Iqbal","sequence":"first","affiliation":[{"name":"1 Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK and 2Department of Statistics, South Parks Road, Oxford, OX1 3TG, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Isaac","family":"Turner","sequence":"additional","affiliation":[{"name":"1 Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK and 2Department of Statistics, South Parks Road, Oxford, OX1 3TG, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gil","family":"McVean","sequence":"additional","affiliation":[{"name":"1 Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK and 2Department of Statistics, South Parks Road, Oxford, OX1 3TG, UK"},{"name":"1 Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK and 2Department of Statistics, South Parks Road, Oxford, OX1 3TG, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,11,19]]},"reference":[{"key":"2023012810224187700_bts673-B1","doi-asserted-by":"crossref","first-page":"3207","DOI":"10.1093\/bioinformatics\/btp579","article-title":"Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data","volume":"25","author":"Degner","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012810224187700_bts673-B2","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1186\/1471-2164-12-425","article-title":"Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica","volume":"12","author":"den Bakker","year":"2011","journal-title":"BMC Genomics"},{"key":"2023012810224187700_bts673-B3","first-page":"133","article-title":"De novo assembly and genotyping of variants using colored de Bruijn graphs","volume":"199","author":"Iqbal","year":"2012","journal-title":"Nat. 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