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

Chi Man Liu; Thomas Wong; Edward Wu; Ruibang Luo; Siu Ming Yiu; Yingrui Li; Bingqiang Wang; Chang Yu; Xiaowen CHU; Kaiyong Zhao; Ruiqiang Li; Tak Wah Lam

doi:10.1093/bioinformatics/bts061

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

Chi Man Liu, Thomas Wong, Edward Wu, Ruibang Luo, Siu Ming Yiu, Yingrui Li, Bingqiang Wang, Chang Yu, Xiaowen CHU, Kaiyong Zhao, Ruiqiang Li^*, Tak Wah Lam

^*Corresponding author for this work

Department of Computer Science

Research output: Contribution to journal › Journal article › peer-review

178 Citations (Scopus)

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.

Original language	English
Article number	bts061
Pages (from-to)	878-879
Number of pages	2
Journal	Bioinformatics
Volume	28
Issue number	6
DOIs	https://doi.org/10.1093/bioinformatics/bts061
Publication status	Published - Mar 2012

Scopus Subject Areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/bts061

Cite this

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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.",

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AU - Li, Yingrui

AU - Wang, Bingqiang

AU - Yu, Chang

AU - CHU, Xiaowen

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AU - Li, Ruiqiang

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

Abstract

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