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Article: SOAP2: An improved ultrafast tool for short read alignment

TitleSOAP2: An improved ultrafast tool for short read alignment
Authors
Li, RYu, CLi, YLam, TWYiu, SMKristiansen, KWang, J
Issue Date2009
PublisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/
Citation
Bioinformatics, 2009, v. 25 n. 15, p. 1966-1967 How to Cite?
DOI: http://dx.doi.org/10.1093/bioinformatics/btp336
AbstractSOAP2 is a significantly improved version of the short oligonucleotide alignment program that both reduces computer memory usage and increases alignment speed at an unprecedented rate. We used a Burrows Wheeler Transformation (BWT) compression index to substitute the seed strategy for indexing the reference sequence in the main memory. We tested it on the whole human genome and found that this new algorithm reduced memory usage from 14.7 to 5.4 GB and improved alignment speed by 20-30 times. SOAP2 is compatible with both single- and paired-end reads. Additionally, this tool now supports multiple text and compressed file formats. A consensus builder has also been developed for consensus assembly and SNP detection from alignment of short reads on a reference genome. © The Author 2009. Published by Oxford University Press. All rights reserved.
Persistent Identifierhttp://hdl.handle.net/10722/89120
ISSN
1367-4803
2023 Impact Factor: 4.4
2023 SCImago Journal Rankings: 2.574
ISI Accession Number ID
WOS:000268107100019
Funding AgencyGrant Number
National Natural Science Foundation of China30725008
Shenzhen local government of China
Danish Natural Science Research Council272-05-0344
272-07-0196
Funding Information:

National Natural Science Foundation of China (30725008); Shenzhen local government of China; Grants from the Danish Natural Science Research Council (272-05-0344 and 272-07-0196).

References
References in Scopus

 

DC FieldValueLanguage
dc.contributor.authorLi, Ren_HK
dc.contributor.authorYu, Cen_HK
dc.contributor.authorLi, Yen_HK
dc.contributor.authorLam, TWen_HK
dc.contributor.authorYiu, SMen_HK
dc.contributor.authorKristiansen, Ken_HK
dc.contributor.authorWang, Jen_HK
dc.date.accessioned2010-09-06T09:52:38Z-
dc.date.available2010-09-06T09:52:38Z-
dc.date.issued2009en_HK
dc.identifier.citationBioinformatics, 2009, v. 25 n. 15, p. 1966-1967en_HK
dc.identifier.issn1367-4803en_HK
dc.identifier.urihttp://hdl.handle.net/10722/89120-
dc.description.abstractSOAP2 is a significantly improved version of the short oligonucleotide alignment program that both reduces computer memory usage and increases alignment speed at an unprecedented rate. We used a Burrows Wheeler Transformation (BWT) compression index to substitute the seed strategy for indexing the reference sequence in the main memory. We tested it on the whole human genome and found that this new algorithm reduced memory usage from 14.7 to 5.4 GB and improved alignment speed by 20-30 times. SOAP2 is compatible with both single- and paired-end reads. Additionally, this tool now supports multiple text and compressed file formats. A consensus builder has also been developed for consensus assembly and SNP detection from alignment of short reads on a reference genome. © The Author 2009. Published by Oxford University Press. All rights reserved.en_HK
dc.languageengen_HK
dc.publisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/en_HK
dc.relation.ispartofBioinformaticsen_HK
dc.rightsBioinformatics. Copyright © Oxford University Press.en_HK
dc.subject.meshComputational Biology - methodsen_HK
dc.subject.meshGenome, Humanen_HK
dc.subject.meshHumansen_HK
dc.subject.meshSequence Alignment - methodsen_HK
dc.subject.meshSequence Analysis, DNA - methodsen_HK
dc.subject.meshSoftwareen_HK
dc.titleSOAP2: An improved ultrafast tool for short read alignmenten_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=1367-4803&volume=25&issue=15&spage=1966&epage=67&date=2009&atitle=SOAP2:+an+Improved+Ultrafast+Tool+for+Short+Read+Alignmenten_HK
dc.identifier.emailLam, TW:twlam@cs.hku.hken_HK
dc.identifier.emailYiu, SM:smyiu@cs.hku.hken_HK
dc.identifier.authorityLam, TW=rp00135en_HK
dc.identifier.authorityYiu, SM=rp00207en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1093/bioinformatics/btp336en_HK
dc.identifier.pmid19497933-
dc.identifier.scopuseid_2-s2.0-67650711615en_HK
dc.identifier.hkuros161313en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-67650711615&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume25en_HK
dc.identifier.issue15en_HK
dc.identifier.spage1966en_HK
dc.identifier.epage1967en_HK
dc.identifier.isiWOS:000268107100019-
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.scopusauthoridLi, R=34975581600en_HK
dc.identifier.scopusauthoridYu, C=25637910500en_HK
dc.identifier.scopusauthoridLi, Y=23766780600en_HK
dc.identifier.scopusauthoridLam, TW=7202523165en_HK
dc.identifier.scopusauthoridYiu, SM=7003282240en_HK
dc.identifier.scopusauthoridKristiansen, K=7102589497en_HK
dc.identifier.scopusauthoridWang, J=36068781200en_HK
dc.identifier.citeulike4774374-
dc.identifier.issnl1367-4803-

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