{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T12:47:45Z","timestamp":1775911665662,"version":"3.50.1"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2016,9,1]],"date-time":"2016-09-01T00:00:00Z","timestamp":1472688000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Microsatellites, also known as short tandem repeats (STRs), are tracts of repetitive DNA sequences containing motifs ranging from two to six bases. Microsatellites are one of the most abundant type of variation in the human genome, after single nucleotide polymorphisms (SNPs) and Indels. Microsatellite analysis has a wide range of applications, including medical genetics, forensics and construction of genetic genealogy. However, microsatellite variations are rarely considered in whole-genome sequencing studies, in large due to a lack of tools capable of analyzing them.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here we present a microsatellite genotyper, optimized for Illumina WGS data, which is both faster and more accurate than other methods previously presented. There are two main ingredients to our improvements. First we reduce the amount of sequencing data necessary for creating microsatellite profiles by using previously aligned sequencing data. Second, we use population information to train microsatellite and individual specific error profiles. By comparing our genotyping results to genotypes generated by capillary electrophoresis we show that our error rates are 50% lower than those of lobSTR, another program specifically developed to determine microsatellite genotypes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>Source code is available on Github: https:\/\/github.com\/DecodeGenetics\/popSTR<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw568","type":"journal-article","created":{"date-parts":[[2016,9,3]],"date-time":"2016-09-03T00:19:48Z","timestamp":1472861988000},"page":"4041-4048","source":"Crossref","is-referenced-by-count":33,"title":["popSTR: population-scale detection of STR variants"],"prefix":"10.1093","volume":"33","author":[{"given":"Sn\u00e6d\u00eds","family":"Kristmundsd\u00f3ttir","sequence":"first","affiliation":[{"name":"deCODE genetics\/Amgen, Reykjav\u00edk University, Reykjav\u00edk, Iceland"}]},{"given":"Brynja D","family":"Sigurp\u00e1lsd\u00f3ttir","sequence":"additional","affiliation":[{"name":"School of Science and Engineering, Reykjav\u00edk University, Reykjav\u00edk, Iceland"}]},{"given":"Birte","family":"Kehr","sequence":"additional","affiliation":[{"name":"deCODE genetics\/Amgen, Reykjav\u00edk University, Reykjav\u00edk, Iceland"}]},{"given":"Bjarni V","family":"Halld\u00f3rsson","sequence":"additional","affiliation":[{"name":"deCODE genetics\/Amgen, Reykjav\u00edk University, Reykjav\u00edk, Iceland"},{"name":"School of Science and Engineering, Reykjav\u00edk University, Reykjav\u00edk, Iceland"}]}],"member":"286","published-online":{"date-parts":[[2016,9,1]]},"reference":[{"key":"2023020207505443000_btw568-B1","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1093\/nar\/27.2.573","article-title":"Tandem repeats finder: a program to analyze dna sequences","volume":"27","author":"Benson","year":"1999","journal-title":"Nucleic Acids Res"},{"key":"2023020207505443000_btw568-B2","volume-title":"Genomes","author":"Brown","year":"2002","edition":"2nd edn"},{"key":"2023020207505443000_btw568-B3","volume-title":"Human Osteology: In Archaeology and Forensic Science","author":"Cox","year":"2000"},{"key":"2023020207505443000_btw568-B4","doi-asserted-by":"crossref","first-page":"11.","DOI":"10.1186\/1471-2105-9-11","article-title":"SeqAn an efficient, generic c\u2009++ library for sequence analysis","volume":"9","author":"D\u00f6ring","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023020207505443000_btw568-B5","doi-asserted-by":"crossref","first-page":"5728","DOI":"10.1093\/nar\/gku212","article-title":"Large-scale analysis of tandem repeat variability in the human genome","volume":"42","author":"Duitama","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020207505443000_btw568-B6","doi-asserted-by":"crossref","first-page":"8884","DOI":"10.1093\/nar\/gku642","article-title":"VNTRseek-a computational tool to detect tandem repeat variants in high-throughput sequencing data","volume":"42","author":"Gelfand","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020207505443000_btw568-B7","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1038\/75514","article-title":"Allegro, a new computer program for multipoint linkage analysis","volume":"25","author":"Gudbjartsson","year":"2000","journal-title":"Nat Genet"},{"key":"2023020207505443000_btw568-B8","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1038\/ng.3247","article-title":"Large-scale whole-genome sequencing of the icelandic population","volume":"47","author":"Gudbjartsson","year":"2015","journal-title":"Nat Genet"},{"key":"2023020207505443000_btw568-B9","doi-asserted-by":"crossref","first-page":"1154","DOI":"10.1101\/gr.135780.111","article-title":"lobstr: A short tandem repeat profiler for personal genomes","volume":"22","author":"Gymrek","year":"2012","journal-title":"Genome Res"},{"key":"2023020207505443000_btw568-B10","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1038\/ng.3461","article-title":"Abundant contribution of short tandem repeats to gene expression variation in humans","volume":"48","author":"Gymrek","year":"2016","journal-title":"Nat. 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Pregl"},{"key":"2023020207505443000_btw568-B19","doi-asserted-by":"crossref","first-page":"1894","DOI":"10.1101\/gr.177774.114","article-title":"The landscape of human str variation","volume":"24","author":"Willems","year":"2014","journal-title":"Genome Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/24\/4041\/49042005\/bioinformatics_33_24_4041.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/24\/4041\/49042005\/bioinformatics_33_24_4041.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T07:52:12Z","timestamp":1675324332000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/24\/4041\/2525679"}},"subtitle":[],"editor":[{"given":"Gunnar","family":"Ratsch","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2016,9,1]]},"references-count":19,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2017,12,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw568","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,12,15]]},"published":{"date-parts":[[2016,9,1]]}}}