Show simple item record

dc.contributor.authorBalzer, Susanne Mignoneng
dc.contributor.authorMalde, Ketileng
dc.contributor.authorLanzén, Anderseng
dc.contributor.authorSharma, Animesheng
dc.contributor.authorJonassen, Ingeeng
dc.date.accessioned2013-10-30T12:27:27Z
dc.date.available2013-10-30T12:27:27Z
dc.date.issued2010eng
dc.identifier.issn1367-4803eng
dc.identifier.urihttp://hdl.handle.net/1956/7456
dc.descriptionECCB 2010 CONFERENCE PROCEEDINGS SEPTEMBER 26 TO SEPTEMBER 29, 2010, GHENT, BELGIUM.eng
dc.description.abstract<p><strong>Motivation:</strong> The commercial launch of 454 pyrosequencing in 2005was a milestone in genome sequencing in terms of performance and cost. Throughout the three available releases, average read lengths have increased to ∼500 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.</p> <p><strong>Results:</strong> 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.</p> <p><strong>Availability:</strong> Flowsim is freely available under the General Public License from <a href="http://blog.malde.org/index.php/flowsim/" target="blank">http://blog.malde.org/index.php/flowsim/</a></p>eng
dc.language.isoengeng
dc.publisherOxford University Presseng
dc.relation.ispartof<a href="http://hdl.handle.net/1956/7455" target="blank">Characteristics of Pyrosequencing Data – Analysis, Methods, and Tools</a>eng
dc.rightsAttribution-NonCommercial CC BY-NCeng
dc.rights.urihttp://creativecommons.org/licenses/by-nc/2.5eng
dc.titleCharacteristics of 454 pyrosequencing data—enabling realistic simulation with flowsimeng
dc.typePeer reviewedeng
dc.typeJournal articleeng
dc.rights.holderCopyright The Author(s) 2010. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.type.versionpublishedVersioneng
bora.peerreviewedPeer reviewedeng
bora.journalTitleBioinformaticseng
bibo.volume26eng
bibo.issue18eng
bibo.pageStarti420eng
bibo.pageEndi425eng
bibo.eissn1460-2059eng
bibo.doihttp://dx.doi.org/10.1093/bioinformatics/btq365eng
dc.identifier.doi10.1093/bioinformatics/btq365
dcterms.isPartOfhttp://hdl.handle.net/1956/7455


Files in this item

Thumbnail

This item appears in the following Collection(s)

Show simple item record

Attribution-NonCommercial CC BY-NC
Except where otherwise noted, this item's license is described as Attribution-NonCommercial CC BY-NC