dc.contributor.author | Balzer, Susanne Mignon | eng |
dc.contributor.author | Malde, Ketil | eng |
dc.contributor.author | Lanzén, Anders | eng |
dc.contributor.author | Sharma, Animesh | eng |
dc.contributor.author | Jonassen, Inge | eng |
dc.date.accessioned | 2013-10-30T12:27:27Z | |
dc.date.available | 2013-10-30T12:27:27Z | |
dc.date.issued | 2010 | eng |
dc.identifier.issn | 1367-4803 | en_US |
dc.identifier.issn | 1460-2059 | en_US |
dc.identifier.uri | https://hdl.handle.net/1956/7456 | |
dc.description | ECCB 2010 CONFERENCE PROCEEDINGS SEPTEMBER 26 TO SEPTEMBER 29, 2010, GHENT, BELGIUM. | eng |
dc.description.abstract | Motivation: 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. 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. Availability: Flowsim is freely available under the General Public License from http://blog.malde.org/index.php/flowsim/ | en_US |
dc.language.iso | eng | eng |
dc.publisher | Oxford University Press | en_US |
dc.relation.ispartof | <a href="http://hdl.handle.net/1956/7455" target="blank">Characteristics of Pyrosequencing Data – Analysis, Methods, and Tools</a> | en_US |
dc.rights | Attribution-NonCommercial CC BY-NC | eng |
dc.rights.uri | http://creativecommons.org/licenses/by-nc/2.5 | eng |
dc.title | Characteristics of 454 pyrosequencing data—enabling realistic simulation with flowsim | en_US |
dc.type | Peer reviewed | |
dc.type | Journal article | |
dc.description.version | publishedVersion | en_US |
dc.rights.holder | Copyright 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. | en_US |
dc.identifier.doi | https://doi.org/10.1093/bioinformatics/btq365 | |
dc.source.journal | Bioinformatics | |
dc.source.40 | 26 | |
dc.source.14 | 18 | |
dc.source.pagenumber | i420-i425 | |