File Download
Links for fulltext
(May Require Subscription)
- Publisher Website: 10.1371/journal.pone.0065632
- Scopus: eid_2-s2.0-84878532952
- PMID: 23741504
- WOS: WOS:000319799900217
- Find via
Supplementary
- Citations:
- Appears in Collections:
Article: SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner
Title | SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner |
---|---|
Authors | |
Issue Date | 2013 |
Publisher | Public 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? |
Abstract | To 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 Identifier | http://hdl.handle.net/10722/190304 |
ISSN | 2021 Impact Factor: 3.752 2020 SCImago Journal Rankings: 0.990 |
PubMed Central ID | |
ISI Accession Number ID |
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Luo, R | en_US |
dc.contributor.author | Wong, T | en_US |
dc.contributor.author | Zhu, J | en_US |
dc.contributor.author | Liu, CM | en_US |
dc.contributor.author | Zhu, X | en_US |
dc.contributor.author | Wu, E | en_US |
dc.contributor.author | Lee, LK | en_US |
dc.contributor.author | Lin, H | - |
dc.contributor.author | Zhu, W | - |
dc.contributor.author | Cheung, DWL | - |
dc.contributor.author | Ting, HF | - |
dc.contributor.author | Yiu, SM | - |
dc.contributor.author | Peng, S | - |
dc.contributor.author | Yu, C | - |
dc.contributor.author | Li, Y | - |
dc.contributor.author | Li, R | - |
dc.contributor.author | Lam, TW | - |
dc.date.accessioned | 2013-09-17T15:18:24Z | - |
dc.date.available | 2013-09-17T15:18:24Z | - |
dc.date.issued | 2013 | en_US |
dc.identifier.citation | PLOS ONE, 2013, v. 8 n. 5, p. e65632 | en_US |
dc.identifier.issn | 1932-6203 | - |
dc.identifier.uri | http://hdl.handle.net/10722/190304 | - |
dc.description.abstract | To 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.language | eng | en_US |
dc.publisher | Public Library of Science. The Journal's web site is located at http://www.plosone.org/home.action | - |
dc.relation.ispartof | PLoS ONE | en_US |
dc.rights | This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. | - |
dc.title | SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner | en_US |
dc.type | Article | en_US |
dc.identifier.email | Luo, R: rbluo@hku.hk | en_US |
dc.identifier.email | Lee, LK: lklee@cs.hku.hk | en_US |
dc.identifier.email | Cheung, DWL: dcheung@cs.hku.hk | en_US |
dc.identifier.email | Ting, HF: hfting@cs.hku.hk | - |
dc.identifier.email | Yiu, SM: smyiu@cs.hku.hk | - |
dc.identifier.email | Lam, TW: twlam@cs.hku.hk | - |
dc.identifier.authority | Lee, LK=rp00140 | en_US |
dc.description.nature | published_or_final_version | - |
dc.identifier.doi | 10.1371/journal.pone.0065632 | - |
dc.identifier.pmid | 23741504 | - |
dc.identifier.pmcid | PMC3669295 | - |
dc.identifier.scopus | eid_2-s2.0-84878532952 | - |
dc.identifier.hkuros | 222013 | en_US |
dc.identifier.volume | 8 | en_US |
dc.identifier.issue | 5 | en_US |
dc.identifier.spage | e65632 | en_US |
dc.identifier.epage | e65632 | en_US |
dc.identifier.isi | WOS:000319799900217 | - |
dc.publisher.place | United States | - |
dc.identifier.issnl | 1932-6203 | - |