{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T16:24:29Z","timestamp":1791217469805,"version":"4.1.0"},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Third generation sequencing methods provide longer reads than second generation methods and have distinct error characteristics. While there exist many read simulators for second generation data, there is a very limited choice for third generation data.<\/jats:p>\n               <jats:p>Results: We analyzed public data from Pacific Biosciences (PacBio) SMRT sequencing, developed an error model and implemented it in a new read simulator called SimLoRD. It offers options to choose the read length distribution and to model error probabilities depending on the number of passes through the sequencer. The new error model makes SimLoRD the most realistic SMRT read simulator available.<\/jats:p>\n               <jats:p>Availability and Implementation: SimLoRD is available open source at http:\/\/bitbucket.org\/genomeinformatics\/simlord\/ and installable via Bioconda ( http:\/\/bioconda.github.io ).<\/jats:p>\n               <jats:p>Contact: \u00a0Bianca.Stoecker@uni-due.de or Sven.Rahmann@uni-due.de .<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw286","type":"journal-article","created":{"date-parts":[[2016,5,11]],"date-time":"2016-05-11T02:22:51Z","timestamp":1462933371000},"page":"2704-2706","source":"Crossref","is-referenced-by-count":100,"title":["SimLoRD: Simulation of Long Read Data"],"prefix":"10.1093","volume":"32","author":[{"given":"Bianca K.","family":"St\u00f6cker","sequence":"first","affiliation":[{"name":"1 Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen, Essen, 45147, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johannes","family":"K\u00f6ster","sequence":"additional","affiliation":[{"name":"2 Life Sciences, Centrum Wiskunde & Informatica (CWI), Amsterdam 1098 XG, The Netherlands"},{"name":"3 Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sven","family":"Rahmann","sequence":"additional","affiliation":[{"name":"1 Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen, Essen, 45147, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2016,5,10]]},"reference":[{"key":"2023020112590229900_btw286-B1","doi-asserted-by":"crossref","first-page":"238.","DOI":"10.1186\/1471-2105-13-238","article-title":"Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory","volume":"13","author":"Chaisson","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"2023020112590229900_btw286-B2","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1126\/science.1162986","article-title":"Real-time DNA sequencing from single polymerase molecules","volume":"323","author":"Eid","year":"2009","journal-title":"Science"},{"key":"2023020112590229900_btw286-B3","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1093\/bioinformatics\/btr708","article-title":"ART: a next-generation sequencing read simulator","volume":"28","author":"Huang","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020112590229900_btw286-B4","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1093\/bioinformatics\/bts649","article-title":"PBSIM: PacBio reads simulator \u2013 toward accurate genome assembly","volume":"29","author":"Ono","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020112590229900_btw286-B5","doi-asserted-by":"crossref","first-page":"533.","DOI":"10.1186\/1756-0500-7-533","article-title":"FASTQSim: platform-independent data characterization and in silico read generation for NGS datasets","volume":"7","author":"Shcherbina","year":"2014","journal-title":"BMC Res Notes"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/17\/2704\/49022507\/bioinformatics_32_17_2704.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/17\/2704\/49022507\/bioinformatics_32_17_2704.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T22:58:41Z","timestamp":1675292321000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/17\/2704\/2450740"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,5,10]]},"references-count":5,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2016,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw286","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,9,1]]},"published":{"date-parts":[[2016,5,10]]}}}