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Article: SOAP3: ultra-fast GPU-based parallel alignment tool for short reads

TitleSOAP3: ultra-fast GPU-based parallel alignment tool for short reads
Authors
KeywordsArticle
Computer program
Dna sequence
High throughput sequencing
Human genome
Issue Date2012
PublisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/
Citation
Bioinformatics, 2012, v. 28 n. 6, p. 878-879 How to Cite?
Abstract
SOAP3 is the first short read alignment tool that leverages the multi-processors in a graphic processing unit (GPU) to achieve a drastic improvement in speed. We adapted the compressed full-text index (BWT) used by SOAP2 in view of the advantages and disadvantages of GPU. When tested with millions of Illumina Hiseq 2000 length-100 bp reads, SOAP3 takes < 30 s to align a million read pairs onto the human reference genome and is at least 7.5 and 20 times faster than BWA and Bowtie, respectively. For aligning reads with up to four mismatches, SOAP3 aligns slightly more reads than BWA and Bowtie; this is because SOAP3, unlike BWA and Bowtie, is not heuristic-based and always reports all answers. © The Author 2012. Published by Oxford University Press. All rights reserved.
Persistent Identifierhttp://hdl.handle.net/10722/165844
ISSN
2013 Impact Factor: 4.621
ISI Accession Number ID

 

Author Affiliations
  1. The University of Hong Kong
  2. Hong Kong Baptist University
  3. Peking University
DC FieldValueLanguage
dc.contributor.authorLiu, CMen_US
dc.contributor.authorWong, Ten_US
dc.contributor.authorWu, Een_US
dc.contributor.authorLuo, Ren_US
dc.contributor.authorYiu, SMen_US
dc.contributor.authorLi, Yen_US
dc.contributor.authorWang, Ben_US
dc.contributor.authorYu, Cen_US
dc.contributor.authorChu, Xen_US
dc.contributor.authorZhao, Ken_US
dc.contributor.authorLi, Ren_US
dc.contributor.authorLam, TW-
dc.date.accessioned2012-09-20T08:24:29Z-
dc.date.available2012-09-20T08:24:29Z-
dc.date.issued2012en_US
dc.identifier.citationBioinformatics, 2012, v. 28 n. 6, p. 878-879en_US
dc.identifier.issn1367-4803-
dc.identifier.urihttp://hdl.handle.net/10722/165844-
dc.description.abstractSOAP3 is the first short read alignment tool that leverages the multi-processors in a graphic processing unit (GPU) to achieve a drastic improvement in speed. We adapted the compressed full-text index (BWT) used by SOAP2 in view of the advantages and disadvantages of GPU. When tested with millions of Illumina Hiseq 2000 length-100 bp reads, SOAP3 takes < 30 s to align a million read pairs onto the human reference genome and is at least 7.5 and 20 times faster than BWA and Bowtie, respectively. For aligning reads with up to four mismatches, SOAP3 aligns slightly more reads than BWA and Bowtie; this is because SOAP3, unlike BWA and Bowtie, is not heuristic-based and always reports all answers. © The Author 2012. Published by Oxford University Press. All rights reserved.-
dc.languageengen_US
dc.publisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/-
dc.relation.ispartofBioinformaticsen_US
dc.subjectArticle-
dc.subjectComputer program-
dc.subjectDna sequence-
dc.subjectHigh throughput sequencing-
dc.subjectHuman genome-
dc.titleSOAP3: ultra-fast GPU-based parallel alignment tool for short readsen_US
dc.typeArticleen_US
dc.identifier.emailLiu, CM: cmliu@cs.hku.hken_US
dc.identifier.emailWong, T: kfwong@cs.hku.hken_US
dc.identifier.emailWu, E: mkewu@hku.hken_US
dc.identifier.emailLuo, R: rbluo@hku.hken_US
dc.identifier.emailYiu, SM: smyiu@cs.hku.hken_US
dc.identifier.emailLi, R: liruiqiang@gmail.comen_US
dc.identifier.emailLam, TW: hresltk@hkucc.hku.hk-
dc.identifier.authorityYiu, SM=rp00207en_US
dc.identifier.authorityLam, TW=rp00135en_US
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1093/bioinformatics/bts061-
dc.identifier.pmid22285832-
dc.identifier.scopuseid_2-s2.0-84859048351-
dc.identifier.hkuros208102en_US
dc.identifier.volume28en_US
dc.identifier.issue6-
dc.identifier.spage878en_US
dc.identifier.epage879en_US
dc.identifier.eissn1460-2059-
dc.identifier.isiWOS:000301972900018-
dc.publisher.placeUnited Kingdom-
dc.identifier.citeulike10282959-

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