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- Publisher Website: 10.1093/bioinformatics/bts061
- Scopus: eid_2-s2.0-84859048351
- PMID: 22285832
- WOS: WOS:000301972900018
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Article: SOAP3: ultra-fast GPU-based parallel alignment tool for short reads
Title | SOAP3: ultra-fast GPU-based parallel alignment tool for short reads |
---|---|
Authors | |
Keywords | Article Computer program Dna sequence High throughput sequencing Human genome |
Issue Date | 2012 |
Publisher | Oxford 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 Identifier | http://hdl.handle.net/10722/165844 |
ISSN | 2023 Impact Factor: 4.4 2023 SCImago Journal Rankings: 2.574 |
ISI Accession Number ID |
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Liu, CM | en_US |
dc.contributor.author | Wong, T | en_US |
dc.contributor.author | Wu, E | en_US |
dc.contributor.author | Luo, R | en_US |
dc.contributor.author | Yiu, SM | en_US |
dc.contributor.author | Li, Y | en_US |
dc.contributor.author | Wang, B | en_US |
dc.contributor.author | Yu, C | en_US |
dc.contributor.author | Chu, X | en_US |
dc.contributor.author | Zhao, K | en_US |
dc.contributor.author | Li, R | en_US |
dc.contributor.author | Lam, TW | - |
dc.date.accessioned | 2012-09-20T08:24:29Z | - |
dc.date.available | 2012-09-20T08:24:29Z | - |
dc.date.issued | 2012 | en_US |
dc.identifier.citation | Bioinformatics, 2012, v. 28 n. 6, p. 878-879 | en_US |
dc.identifier.issn | 1367-4803 | - |
dc.identifier.uri | http://hdl.handle.net/10722/165844 | - |
dc.description.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. | - |
dc.language | eng | en_US |
dc.publisher | Oxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/ | - |
dc.relation.ispartof | Bioinformatics | en_US |
dc.subject | Article | - |
dc.subject | Computer program | - |
dc.subject | Dna sequence | - |
dc.subject | High throughput sequencing | - |
dc.subject | Human genome | - |
dc.title | SOAP3: ultra-fast GPU-based parallel alignment tool for short reads | en_US |
dc.type | Article | en_US |
dc.identifier.email | Liu, CM: cmliu@cs.hku.hk | en_US |
dc.identifier.email | Wong, T: kfwong@cs.hku.hk | en_US |
dc.identifier.email | Wu, E: mkewu@hku.hk | en_US |
dc.identifier.email | Luo, R: rbluo@hku.hk | en_US |
dc.identifier.email | Yiu, SM: smyiu@cs.hku.hk | en_US |
dc.identifier.email | Li, R: liruiqiang@gmail.com | en_US |
dc.identifier.email | Lam, TW: hresltk@hkucc.hku.hk | - |
dc.identifier.authority | Yiu, SM=rp00207 | en_US |
dc.identifier.authority | Lam, TW=rp00135 | en_US |
dc.description.nature | link_to_OA_fulltext | - |
dc.identifier.doi | 10.1093/bioinformatics/bts061 | - |
dc.identifier.pmid | 22285832 | - |
dc.identifier.scopus | eid_2-s2.0-84859048351 | - |
dc.identifier.hkuros | 208102 | en_US |
dc.identifier.volume | 28 | en_US |
dc.identifier.issue | 6 | - |
dc.identifier.spage | 878 | en_US |
dc.identifier.epage | 879 | en_US |
dc.identifier.eissn | 1460-2059 | - |
dc.identifier.isi | WOS:000301972900018 | - |
dc.publisher.place | United Kingdom | - |
dc.identifier.citeulike | 10282959 | - |