{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,24]],"date-time":"2026-01-24T07:35:01Z","timestamp":1769240101569,"version":"3.49.0"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2220,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The commercial launch of 454 pyrosequencing in 2005 was a milestone in genome sequencing in terms of performance and cost. Throughout the three available releases, average read lengths have increased to \u223c500 base pairs and are thus approaching read lengths obtained from traditional Sanger sequencing. Study design of sequencing projects would benefit from being able to simulate experiments.<\/jats:p>\n               <jats:p>Results: We explore 454 raw data to investigate its characteristics and derive empirical distributions for the flow values generated by pyrosequencing. Based on our findings, we implement Flowsim, a simulator that generates realistic pyrosequencing data files of arbitrary size from a given set of input DNA sequences. We finally use our simulator to examine the impact of sequence lengths on the results of concrete whole-genome assemblies, and we suggest its use in planning of sequencing projects, benchmarking of assembly methods and other fields.<\/jats:p>\n               <jats:p>Availability: Flowsim is freely available under the General Public License from http:\/\/blog.malde.org\/index.php\/flowsim\/<\/jats:p>\n               <jats:p>Contact: \u00a0susanne.balzer@imr.no; ketil.malde@imr.no<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq365","type":"journal-article","created":{"date-parts":[[2010,9,7]],"date-time":"2010-09-07T17:41:46Z","timestamp":1283881306000},"page":"i420-i425","source":"Crossref","is-referenced-by-count":116,"title":["Characteristics of 454 pyrosequencing data\u2014enabling realistic simulation with flowsim"],"prefix":"10.1093","volume":"26","author":[{"given":"Susanne","family":"Balzer","sequence":"first","affiliation":[{"name":"1 Institute of Marine Research, PO Box 1870, N\u22125817, 2Department of Informatics, University of Bergen, PO Box 7803, N-5020, 3Computational Biology Unit, Bergen Center for Computational Science, Thorm\u00f8hlensgate 55, N-5008 and 4Department of Biology, University of Bergen, PO Box 7803, N-5020, Bergen"},{"name":"1 Institute of Marine Research, PO Box 1870, N\u22125817, 2Department of Informatics, University of Bergen, PO Box 7803, N-5020, 3Computational Biology Unit, Bergen Center for Computational Science, Thorm\u00f8hlensgate 55, N-5008 and 4Department of Biology, University of Bergen, PO Box 7803, N-5020, Bergen"}]},{"given":"Ketil","family":"Malde","sequence":"additional","affiliation":[{"name":"1 Institute of Marine Research, PO Box 1870, N\u22125817, 2Department of Informatics, University of Bergen, PO Box 7803, N-5020, 3Computational Biology Unit, Bergen Center for Computational Science, Thorm\u00f8hlensgate 55, N-5008 and 4Department of Biology, University of Bergen, PO Box 7803, N-5020, Bergen"}]},{"given":"Anders","family":"Lanz\u00e9n","sequence":"additional","affiliation":[{"name":"1 Institute of Marine Research, PO Box 1870, N\u22125817, 2Department of Informatics, University of Bergen, PO Box 7803, N-5020, 3Computational Biology Unit, Bergen Center for Computational Science, Thorm\u00f8hlensgate 55, N-5008 and 4Department of Biology, University of Bergen, PO Box 7803, N-5020, Bergen"},{"name":"1 Institute of Marine Research, PO Box 1870, N\u22125817, 2Department of Informatics, University of Bergen, PO Box 7803, N-5020, 3Computational Biology Unit, Bergen Center for Computational Science, Thorm\u00f8hlensgate 55, N-5008 and 4Department of Biology, University of Bergen, PO Box 7803, N-5020, Bergen"}]},{"given":"Animesh","family":"Sharma","sequence":"additional","affiliation":[{"name":"1 Institute of Marine Research, PO Box 1870, N\u22125817, 2Department of Informatics, University of Bergen, PO Box 7803, N-5020, 3Computational Biology Unit, Bergen Center for Computational Science, Thorm\u00f8hlensgate 55, N-5008 and 4Department of Biology, University of Bergen, PO Box 7803, N-5020, Bergen"}]},{"given":"Inge","family":"Jonassen","sequence":"additional","affiliation":[{"name":"1 Institute of Marine Research, PO Box 1870, N\u22125817, 2Department of Informatics, University of Bergen, PO Box 7803, N-5020, 3Computational Biology Unit, Bergen Center for Computational Science, Thorm\u00f8hlensgate 55, N-5008 and 4Department of Biology, University of Bergen, PO Box 7803, N-5020, Bergen"},{"name":"1 Institute of Marine Research, PO Box 1870, N\u22125817, 2Department of Informatics, University of Bergen, PO Box 7803, N-5020, 3Computational Biology Unit, Bergen Center for Computational Science, Thorm\u00f8hlensgate 55, N-5008 and 4Department of Biology, University of Bergen, PO Box 7803, N-5020, Bergen"}]}],"member":"286","published-online":{"date-parts":[[2010,9,4]]},"reference":[{"key":"2023012508245178700_B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. 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