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Article: SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner

TitleSOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner
Authors
Issue Date2013
PublisherPublic Library of Science. The Journal's web site is located at http://www.plosone.org/home.action
Citation
PLOS ONE, 2013, v. 8 n. 5, p. e65632 How to Cite?
AbstractTo tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, CUSHAW2, GEM and GPU-based aligners BarraCUDA and CUSHAW, SOAP3-dp was found to be two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate (FDR) on Illumina reads with different lengths. Transcending its predecessor SOAP3, which does not allow gapped alignment, SOAP3-dp by default tolerates alignment similarity as low as 60%. Real data evaluation using human genome demonstrates SOAP3-dp's power to enable more authentic variants and longer Indels to be discovered. Fosmid sequencing shows a 9.1% FDR on newly discovered deletions. SOAP3-dp natively supports BAM file format and provides the same scoring scheme as BWA, which enables it to be integrated into existing analysis pipelines. SOAP3-dp has been deployed on Amazon-EC2, NIH-Biowulf and Tianhe-1A.
Persistent Identifierhttp://hdl.handle.net/10722/190304
ISSN
2015 Impact Factor: 3.057
2015 SCImago Journal Rankings: 1.395
PubMed Central ID
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorLuo, Ren_US
dc.contributor.authorWong, Ten_US
dc.contributor.authorZhu, Jen_US
dc.contributor.authorLiu, CMen_US
dc.contributor.authorZhu, Xen_US
dc.contributor.authorWu, Een_US
dc.contributor.authorLee, LKen_US
dc.contributor.authorLin, H-
dc.contributor.authorZhu, W-
dc.contributor.authorCheung, DWL-
dc.contributor.authorTing, HF-
dc.contributor.authorYiu, SM-
dc.contributor.authorPeng, S-
dc.contributor.authorYu, C-
dc.contributor.authorLi, Y-
dc.contributor.authorLi, R-
dc.contributor.authorLam, TW-
dc.date.accessioned2013-09-17T15:18:24Z-
dc.date.available2013-09-17T15:18:24Z-
dc.date.issued2013en_US
dc.identifier.citationPLOS ONE, 2013, v. 8 n. 5, p. e65632en_US
dc.identifier.issn1932-6203-
dc.identifier.urihttp://hdl.handle.net/10722/190304-
dc.description.abstractTo tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, CUSHAW2, GEM and GPU-based aligners BarraCUDA and CUSHAW, SOAP3-dp was found to be two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate (FDR) on Illumina reads with different lengths. Transcending its predecessor SOAP3, which does not allow gapped alignment, SOAP3-dp by default tolerates alignment similarity as low as 60%. Real data evaluation using human genome demonstrates SOAP3-dp's power to enable more authentic variants and longer Indels to be discovered. Fosmid sequencing shows a 9.1% FDR on newly discovered deletions. SOAP3-dp natively supports BAM file format and provides the same scoring scheme as BWA, which enables it to be integrated into existing analysis pipelines. SOAP3-dp has been deployed on Amazon-EC2, NIH-Biowulf and Tianhe-1A.-
dc.languageengen_US
dc.publisherPublic Library of Science. The Journal's web site is located at http://www.plosone.org/home.action-
dc.relation.ispartofPLOS ONEen_US
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.titleSOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligneren_US
dc.typeArticleen_US
dc.identifier.emailLuo, R: rbluo@hku.hken_US
dc.identifier.emailLee, LK: lklee@cs.hku.hken_US
dc.identifier.emailCheung, DWL: dcheung@cs.hku.hken_US
dc.identifier.emailTing, HF: hfting@cs.hku.hk-
dc.identifier.emailYiu, SM: smyiu@cs.hku.hk-
dc.identifier.emailLam, TW: twlam@cs.hku.hk-
dc.identifier.authorityLee, LK=rp00140en_US
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1371/journal.pone.0065632-
dc.identifier.pmid23741504-
dc.identifier.pmcidPMC3669295-
dc.identifier.scopuseid_2-s2.0-84878532952-
dc.identifier.hkuros222013en_US
dc.identifier.volume8en_US
dc.identifier.issue5en_US
dc.identifier.spagee65632en_US
dc.identifier.epagee65632en_US
dc.identifier.isiWOS:000319799900217-
dc.publisher.placeUnited States-

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