{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T12:25:49Z","timestamp":1783427149032,"version":"3.54.6"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2020,9,25]],"date-time":"2020-09-25T00:00:00Z","timestamp":1600992000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"MEXT KAKENHI","award":["JP24680031"],"award-info":[{"award-number":["JP24680031"]}]},{"name":"MEXT KAKENHI","award":["JP16H05879"],"award-info":[{"award-number":["JP16H05879"]}]},{"name":"MEXT KAKENHI","award":["JP20H00624"],"award-info":[{"award-number":["JP20H00624"]}]},{"name":"MEXT KAKENHI","award":["JP16H06279"],"award-info":[{"award-number":["JP16H06279"]}]},{"name":"MEXT KAKENHI","award":["JP25240044"],"award-info":[{"award-number":["JP25240044"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Recent advances in high-throughput long-read sequencers, such as PacBio and Oxford Nanopore sequencers, produce longer reads with more errors than short-read sequencers. In addition to the high error rates of reads, non-uniformity of errors leads to difficulties in various downstream analyses using long reads. Many useful simulators, which characterize long-read error patterns and simulate them, have been developed. However, there is still room for improvement in the simulation of the non-uniformity of errors.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>To capture characteristics of errors in reads for long-read sequencers, here, we introduce a generative model for quality scores, in which a hidden Markov Model with a latest model selection method, called factorized information criteria, is utilized. We evaluated our developed simulator from various points, indicating that our simulator successfully simulates reads that are consistent with real reads.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The source codes of PBSIM2 are freely available from https:\/\/github.com\/yukiteruono\/pbsim2.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa835","type":"journal-article","created":{"date-parts":[[2020,9,11]],"date-time":"2020-09-11T11:14:03Z","timestamp":1599822843000},"page":"589-595","source":"Crossref","is-referenced-by-count":141,"title":["PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores"],"prefix":"10.1093","volume":"37","author":[{"given":"Yukiteru","family":"Ono","sequence":"first","affiliation":[{"name":"Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo , Kashiwa 277-8561, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kiyoshi","family":"Asai","sequence":"additional","affiliation":[{"name":"Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo , Kashiwa 277-8561, Japan"},{"name":"Artificial Intelligence Research Center (AIRC), National Institute of Advanced Industrial Science and Technology (AIST) , Tokyo 135\u20130064, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9466-1034","authenticated-orcid":false,"given":"Michiaki","family":"Hamada","sequence":"additional","affiliation":[{"name":"Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University , Tokyo 169\u20138555, Japan"},{"name":"Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST) , Tokyo 169\u20138555, Japan"},{"name":"Institute for Medical-oriented Structural Biology, Waseda University , Tokyo 162\u20138480, Japan"},{"name":"Graduate School of Medicine, Nippon Medical School , Tokyo 113\u20138602, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,9,25]]},"reference":[{"key":"2023051704112100000_btaa835-B1","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1093\/bfgp\/elz033","article-title":"A broad survey of DNA sequence data simulation tools","volume":"19","author":"Alosaimi","year":"2020","journal-title":"Brief. 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