SOAP3: ultra-fast GPU-based parallel alignment tool for short reads

Liu, Chi-Man, Wong, Thomas, Wu, Edward, Luo, Ruibang, Yiu, Siu-Ming, Li, Yingrui, Wang, Bingqiang, Yu, Chang, Chu, Xiaowen, Zhao, Kaiyong, Li, Ruiqiang and Lam, Tak-Wah (2012) SOAP3: ultra-fast GPU-based parallel alignment tool for short reads. Bioinformatics, 28 6: 878-879. doi:10.1093/bioinformatics/bts061

Author Liu, Chi-Man
Wong, Thomas
Wu, Edward
Luo, Ruibang
Yiu, Siu-Ming
Li, Yingrui
Wang, Bingqiang
Yu, Chang
Chu, Xiaowen
Zhao, Kaiyong
Li, Ruiqiang
Lam, Tak-Wah
Title SOAP3: ultra-fast GPU-based parallel alignment tool for short reads
Journal name Bioinformatics   Check publisher's open access policy
ISSN 1367-4803
Publication date 2012-03-15
Sub-type Article (original research)
DOI 10.1093/bioinformatics/bts061
Open Access Status Not Open Access
Volume 28
Issue 6
Start page 878
End page 879
Total pages 2
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Language eng
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.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Institute for Molecular Bioscience - Publications
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