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Conference Paper: IDBA - A practical iterative De Bruijn graph De Novo assembler

TitleIDBA - A practical iterative De Bruijn graph De Novo assembler
Authors
KeywordsDe Bruijn graph
De Novo assembly
High throughput short reads
Mate-pair
String graph
Issue Date2010
PublisherSpringer Verlag. The Journal's web site is located at http://springerlink.com/content/105633/
Citation
The 14th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2010), Lisbon, Portugal, 25-28 April 2010. In Lecture Notes in Computer Science, 2010, v. 6044, p. 426-440 How to Cite?
Abstract
The de Bruijn graph assembly approach breaks reads into k-mers before assembling them into contigs. The string graph approach forms contigs by connecting two reads with k or more overlapping nucleotides. Both approaches must deal with the following problems: false-positive vertices, due to erroneous reads; gap problem, due to non-uniform coverage; branching problem, due to erroneous reads and repeat regions. A proper choice of k is crucial but for single k there is always a trade-off: a small k favors the situation of erroneous reads and non-uniform coverage, and a large k favors short repeat regions. We propose an iterative de Bruijn graph approach iterating from small to large k exploring the advantages of the in between values. Our IDBA outperforms the existing algorithms by constructing longer contigs with similar accuracy and using less memory, both with real and simulated data. The running time of the algorithm is comparable to existing algorithms. © Springer-Verlag Berlin Heidelberg 2010.
DescriptionLNCS v. 6044 is conference proceedings of 14th RECOMB 2010
Persistent Identifierhttp://hdl.handle.net/10722/129571
ISSN
2013 SCImago Journal Rankings: 0.310
References

 

Author Affiliations
  1. The University of Hong Kong
DC FieldValueLanguage
dc.contributor.authorPeng, Yen_HK
dc.contributor.authorLeung, HCMen_HK
dc.contributor.authorYiu, SMen_HK
dc.contributor.authorChin, FYLen_HK
dc.date.accessioned2010-12-23T08:39:23Z-
dc.date.available2010-12-23T08:39:23Z-
dc.date.issued2010en_HK
dc.identifier.citationThe 14th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2010), Lisbon, Portugal, 25-28 April 2010. In Lecture Notes in Computer Science, 2010, v. 6044, p. 426-440en_HK
dc.identifier.issn0302-9743en_HK
dc.identifier.urihttp://hdl.handle.net/10722/129571-
dc.descriptionLNCS v. 6044 is conference proceedings of 14th RECOMB 2010-
dc.description.abstractThe de Bruijn graph assembly approach breaks reads into k-mers before assembling them into contigs. The string graph approach forms contigs by connecting two reads with k or more overlapping nucleotides. Both approaches must deal with the following problems: false-positive vertices, due to erroneous reads; gap problem, due to non-uniform coverage; branching problem, due to erroneous reads and repeat regions. A proper choice of k is crucial but for single k there is always a trade-off: a small k favors the situation of erroneous reads and non-uniform coverage, and a large k favors short repeat regions. We propose an iterative de Bruijn graph approach iterating from small to large k exploring the advantages of the in between values. Our IDBA outperforms the existing algorithms by constructing longer contigs with similar accuracy and using less memory, both with real and simulated data. The running time of the algorithm is comparable to existing algorithms. © Springer-Verlag Berlin Heidelberg 2010.en_HK
dc.languageengen_US
dc.publisherSpringer Verlag. The Journal's web site is located at http://springerlink.com/content/105633/en_HK
dc.relation.ispartofLecture Notes in Computer Scienceen_HK
dc.rightsThe original publication is available at www.springerlink.com-
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.subjectDe Bruijn graphen_HK
dc.subjectDe Novo assemblyen_HK
dc.subjectHigh throughput short readsen_HK
dc.subjectMate-pairen_HK
dc.subjectString graphen_HK
dc.titleIDBA - A practical iterative De Bruijn graph De Novo assembleren_HK
dc.typeConference_Paperen_HK
dc.identifier.emailLeung, HCM:cmleung2@cs.hku.hken_HK
dc.identifier.emailYiu, SM:smyiu@cs.hku.hken_HK
dc.identifier.emailChin, FYL:chin@cs.hku.hken_HK
dc.identifier.authorityLeung, HCM=rp00144en_HK
dc.identifier.authorityYiu, SM=rp00207en_HK
dc.identifier.authorityChin, FYL=rp00105en_HK
dc.description.naturepostprint-
dc.identifier.doi10.1007/978-3-642-12683-3_28en_HK
dc.identifier.scopuseid_2-s2.0-78650270346en_HK
dc.identifier.hkuros178332en_US
dc.identifier.hkuros169727-
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-78650270346&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume6044 LNBIen_HK
dc.identifier.spage426en_HK
dc.identifier.epage440en_HK
dc.publisher.placeGermanyen_HK
dc.description.otherThe 14th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2010), Lisbon, Portugal, 25-28 April 2010. In Lecture Notes in Computer Science, 2010, v. 6044, p. 426-440-
dc.identifier.scopusauthoridPeng, Y=30267885400en_HK
dc.identifier.scopusauthoridLeung, HCM=35233742700en_HK
dc.identifier.scopusauthoridYiu, SM=7003282240en_HK
dc.identifier.scopusauthoridChin, FYL=7005101915en_HK
dc.identifier.citeulike7896392-

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