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

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TitleSOAP3: ultra-fast GPU-based parallel alignment tool for short reads
AuthorsLiu, CM1
Wong, T1
Wu, E1
Luo, R1
Yiu, SM1
Li, Y
Wang, B
Yu, C
Chu, X2
Zhao, K2
Li, R3
Lam, TW1
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/
CitationBioinformatics, 2012, v. 28 n. 6, p. 878-879 [How to Cite?]
DOI: http://dx.doi.org/10.1093/bioinformatics/bts061
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.
ISSN1367-4803
2011 Impact Factor: 5.468
2011 SCImago Journal Rankings: 1.118
DOIhttp://dx.doi.org/10.1093/bioinformatics/bts061
DC Field
Value
dc.contributor.authorLiu, CM
dc.contributor.authorWong, T
dc.contributor.authorWu, E
dc.contributor.authorLuo, R
dc.contributor.authorYiu, SM
dc.contributor.authorLi, Y
dc.contributor.authorWang, B
dc.contributor.authorYu, C
dc.contributor.authorChu, X
dc.contributor.authorZhao, K
dc.contributor.authorLi, R
dc.contributor.authorLam, TW
dc.date.accessioned2012-09-20T08:24:29Z
dc.date.available2012-09-20T08:24:29Z
dc.date.issued2012
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.description.natureLink_to_subscribed_fulltext
dc.identifier.citationBioinformatics, 2012, v. 28 n. 6, p. 878-879 [How to Cite?]
DOI: http://dx.doi.org/10.1093/bioinformatics/bts061
dc.identifier.citeulike10282959
dc.identifier.doihttp://dx.doi.org/10.1093/bioinformatics/bts061
dc.identifier.epage879
dc.identifier.hkuros208102
dc.identifier.issn1367-4803
2011 Impact Factor: 5.468
2011 SCImago Journal Rankings: 1.118
dc.identifier.issue6
dc.identifier.scopuseid_2-s2.0-84859048351
dc.identifier.spage878
dc.identifier.urihttp://hdl.handle.net/10722/165844
dc.identifier.volume28
dc.languageeng
dc.publisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/
dc.publisher.placeUnited Kingdom
dc.relation.ispartofBioinformatics
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 reads
dc.typeArticle
Author Affiliations
  1. The University of Hong Kong
  2. Hong Kong Baptist University
  3. Peking University