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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
2013 Impact Factor: 4.621
 
DOIhttp://dx.doi.org/10.1093/bioinformatics/bts061
 
ISI Accession Number IDWOS:000301972900018
 
DC FieldValue
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.eissn1460-2059
 
dc.identifier.epage879
 
dc.identifier.hkuros208102
 
dc.identifier.isiWOS:000301972900018
 
dc.identifier.issn1367-4803
2013 Impact Factor: 4.621
 
dc.identifier.issue6
 
dc.identifier.pmid22285832
 
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
 
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<contributor.author>Wong, T</contributor.author>
<contributor.author>Wu, E</contributor.author>
<contributor.author>Luo, R</contributor.author>
<contributor.author>Yiu, SM</contributor.author>
<contributor.author>Li, Y</contributor.author>
<contributor.author>Wang, B</contributor.author>
<contributor.author>Yu, C</contributor.author>
<contributor.author>Chu, X</contributor.author>
<contributor.author>Zhao, K</contributor.author>
<contributor.author>Li, R</contributor.author>
<contributor.author>Lam, TW</contributor.author>
<date.accessioned>2012-09-20T08:24:29Z</date.accessioned>
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Author Affiliations
  1. The University of Hong Kong
  2. Hong Kong Baptist University
  3. Peking University