{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,4]],"date-time":"2026-07-04T02:09:23Z","timestamp":1783130963786,"version":"3.54.6"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2678,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Here, we present a method for estimating the frequencies of SNP alleles present within pooled samples of DNA using high-throughput short-read sequencing. The method was tested on real data from six strains of the highly monomorphic pathogen Salmonella Paratyphi A, sequenced individually and in a pool. A variety of read mapping and quality-weighting procedures were tested to determine the optimal parameters, which afforded \u226580% sensitivity of SNP detection and strong correlation with true SNP frequency at poolwide read depth of 40\u00d7, declining only slightly at read depths 20\u201340\u00d7.<\/jats:p>\n               <jats:p>Availability: The method was implemented in Perl and relies on the opensource software Maq for read mapping and SNP calling. The Perl script is freely available from ftp:\/\/ftp.sanger.ac.uk\/pub\/pathogens\/pools\/.<\/jats:p>\n               <jats:p>Contact: \u00a0kh2@sanger.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp344","type":"journal-article","created":{"date-parts":[[2009,6,5]],"date-time":"2009-06-05T00:24:32Z","timestamp":1244161472000},"page":"2074-2075","source":"Crossref","is-referenced-by-count":41,"title":["Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA"],"prefix":"10.1093","volume":"25","author":[{"given":"Kathryn E.","family":"Holt","sequence":"first","affiliation":[{"name":"1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, 2 Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN and 3 Laboratory of Gastrointestinal Pathogens, Centre for Infections, Health Protection Agency, 61 Colindale Avenue, London NW9 5HT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yik Y.","family":"Teo","sequence":"additional","affiliation":[{"name":"1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, 2 Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN and 3 Laboratory of Gastrointestinal Pathogens, Centre for Infections, Health Protection Agency, 61 Colindale Avenue, London NW9 5HT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heng","family":"Li","sequence":"additional","affiliation":[{"name":"1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, 2 Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN and 3 Laboratory of Gastrointestinal Pathogens, Centre for Infections, Health Protection Agency, 61 Colindale Avenue, London NW9 5HT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Satheesh","family":"Nair","sequence":"additional","affiliation":[{"name":"1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, 2 Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN and 3 Laboratory of Gastrointestinal Pathogens, Centre for Infections, Health Protection Agency, 61 Colindale Avenue, London NW9 5HT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gordon","family":"Dougan","sequence":"additional","affiliation":[{"name":"1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, 2 Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN and 3 Laboratory of Gastrointestinal Pathogens, Centre for Infections, Health Protection Agency, 61 Colindale Avenue, London NW9 5HT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Wain","sequence":"additional","affiliation":[{"name":"1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, 2 Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN and 3 Laboratory of Gastrointestinal Pathogens, Centre for Infections, Health Protection Agency, 61 Colindale Avenue, London NW9 5HT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julian","family":"Parkhill","sequence":"additional","affiliation":[{"name":"1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, 2 Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN and 3 Laboratory of Gastrointestinal Pathogens, Centre for Infections, Health Protection Agency, 61 Colindale Avenue, London NW9 5HT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2009,6,3]]},"reference":[{"key":"2023013112091739700_B1","doi-asserted-by":"crossref","first-page":"1008","DOI":"10.1128\/JCM.38.3.1008-1015.2000","article-title":"Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus","volume":"38","author":"Enright","year":"2000","journal-title":"J. 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