{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T16:50:28Z","timestamp":1780419028426,"version":"3.54.1"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: PacBio sequencers produce two types of characteristic reads (continuous long reads: long and high error rate and circular consensus sequencing: short and low error rate), both of which could be useful for de novo assembly of genomes. Currently, there is no available simulator that targets the specific generation of PacBio libraries.<\/jats:p>\n               <jats:p>Results: Our analysis of 13 PacBio datasets showed characteristic features of PacBio reads (e.g. the read length of PacBio reads follows a log-normal distribution). We have developed a read simulator, PBSIM, that captures these features using either a model-based or sampling-based method. Using PBSIM, we conducted several hybrid error correction and assembly tests for PacBio reads, suggesting that a continuous long reads coverage depth of at least 15 in combination with a circular consensus sequencing coverage depth of at least 30 achieved extensive assembly results.<\/jats:p>\n               <jats:p>Availability: PBSIM is freely available from the web under the GNU GPL v2 license (http:\/\/code.google.com\/p\/pbsim\/).<\/jats:p>\n               <jats:p>Contact: \u00a0mhamada@k.u-tokyo.ac.jp<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts649","type":"journal-article","created":{"date-parts":[[2012,11,6]],"date-time":"2012-11-06T03:08:43Z","timestamp":1352171323000},"page":"119-121","source":"Crossref","is-referenced-by-count":298,"title":["PBSIM: PacBio reads simulator\u2014toward accurate genome assembly"],"prefix":"10.1093","volume":"29","author":[{"given":"Yukiteru","family":"Ono","sequence":"first","affiliation":[{"name":"1 Information and Mathematical Science and Bioinformatics Co., Ltd., Toshima-ku, Tokyo 170\u20130013, 2Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277\u20138562 and 3Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135\u20130064, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kiyoshi","family":"Asai","sequence":"additional","affiliation":[{"name":"1 Information and Mathematical Science and Bioinformatics Co., Ltd., Toshima-ku, Tokyo 170\u20130013, 2Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277\u20138562 and 3Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135\u20130064, Japan"},{"name":"1 Information and Mathematical Science and Bioinformatics Co., Ltd., Toshima-ku, Tokyo 170\u20130013, 2Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277\u20138562 and 3Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135\u20130064, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michiaki","family":"Hamada","sequence":"additional","affiliation":[{"name":"1 Information and Mathematical Science and Bioinformatics Co., Ltd., Toshima-ku, Tokyo 170\u20130013, 2Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277\u20138562 and 3Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135\u20130064, Japan"},{"name":"1 Information and Mathematical Science and Bioinformatics Co., Ltd., Toshima-ku, Tokyo 170\u20130013, 2Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277\u20138562 and 3Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135\u20130064, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2012,11,4]]},"reference":[{"key":"2023020303200402600_bts649-B1","doi-asserted-by":"crossref","first-page":"e94","DOI":"10.1093\/nar\/gks251","article-title":"Grinder: a versatile amplicon and shotgun sequence simulator","volume":"40","author":"Angly","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023020303200402600_bts649-B2","doi-asserted-by":"crossref","first-page":"i420","DOI":"10.1093\/bioinformatics\/btq365","article-title":"Characteristics of 454 pyrosequencing data\u2014enabling realistic simulation with flowsim","volume":"26","author":"Balzer","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020303200402600_bts649-B3","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1186\/1471-2164-13-375","article-title":"Pacific biosciences sequencing technology for genotyping and variation discovery in human data","volume":"13","author":"Carneiro","year":"2012","journal-title":"BMC Genomics"},{"key":"2023020303200402600_bts649-B4","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1056\/NEJMoa1012928","article-title":"The origin of the Haitian cholera outbreak strain","volume":"364","author":"Chin","year":"2011","journal-title":"N. 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