{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,3]],"date-time":"2024-08-03T19:37:31Z","timestamp":1722713851241},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Next generation sequencing technologies facilitate genome-wide analysis of several biological processes. We are interested in whole-genome genotyping. To our knowledge, none of the existing single nucleotide polymorphism (SNP) callers consider the quality of the reference genome, which is not necessary for high-quality assemblies of well-studied model organisms. However, most genome projects will remain in draft status with little to no genome assembly improvement due to time and financial constraints. Here, we present a simple yet elegant solution (\u2018ACCUSA\u2019) that considers both the read qualities as well as the reference genome's quality using a Bayesian framework. We demonstrate that ACCUSA is as good as the current SNP calling software in detecting true SNPs. More importantly, ACCUSA does not call spurious SNPs, which originate from a poor reference sequence.<\/jats:p>\n               <jats:p>Availability: ACCUSA is available free of charge to academic users and may be obtained from ftp:\/\/bbc.mdc-berlin.de\/software. ACCUSA is programmed in JAVA 6 and runs on any platform with JAVA support.<\/jats:p>\n               <jats:p>Contact: \u00a0christoph.dieterich@mdc-berlin.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq138","type":"journal-article","created":{"date-parts":[[2010,4,2]],"date-time":"2010-04-02T00:13:12Z","timestamp":1270167192000},"page":"1364-1365","source":"Crossref","is-referenced-by-count":5,"title":["ACCUSA\u2014accurate SNP calling on draft genomes"],"prefix":"10.1093","volume":"26","author":[{"given":"Sebastian","family":"Fr\u00f6hler","sequence":"first","affiliation":[{"name":"Bioinformatics in Quantitative Biology, The Berlin Institute for Medical Systems Biology at the Max Delbr\u00fcck Center for Molecular Medicine, Robert-R\u00f6ssle-Strasse 10, 13125 Berlin-Buch, Germany"}]},{"given":"Christoph","family":"Dieterich","sequence":"additional","affiliation":[{"name":"Bioinformatics in Quantitative Biology, The Berlin Institute for Medical Systems Biology at the Max Delbr\u00fcck Center for Molecular Medicine, Robert-R\u00f6ssle-Strasse 10, 13125 Berlin-Buch, Germany"}]}],"member":"286","published-online":{"date-parts":[[2010,4,1]]},"reference":[{"key":"2023012507510985100_B1","doi-asserted-by":"crossref","first-page":"e105","DOI":"10.1093\/nar\/gkn425","article-title":"Substantial biases in ultra-short read data sets from high-throughput DNA sequencing","volume":"36","author":"Dohm","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012507510985100_B2","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012507510985100_B3","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1038\/nature07743","article-title":"Population genomics of domestic and wild yeasts","volume":"458","author":"Liti","year":"2009","journal-title":"Nature"},{"key":"2023012507510985100_B4","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1038\/70570","article-title":"A general approach to single-nucleotide polymorphism discovery","volume":"23","author":"Marth","year":"1999","journal-title":"Nat. Genet."},{"key":"2023012507510985100_B5","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1038\/nrg2626","article-title":"Sequencing technologies - the next generation","volume":"11","author":"Metzker","year":"2010","journal-title":"Nat. Rev. Genet."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/10\/1364\/48851018\/bioinformatics_26_10_1364.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/10\/1364\/48851018\/bioinformatics_26_10_1364.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T07:51:22Z","timestamp":1674633082000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/10\/1364\/193563"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,4,1]]},"references-count":5,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2010,5,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq138","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,5,15]]},"published":{"date-parts":[[2010,4,1]]}}}