Document Type
Journal Article
Department/Unit
Department of Computer Science
Title
SOAP3: Ultra-fast GPU-based parallel alignment tool for short reads
Language
English
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.
Publication Date
2012
Source Publication Title
Bioinformatics
Volume
28
Issue
6
Start Page
878
End Page
879
Publisher
Oxford University Press
DOI
10.1093/bioinformatics/bts061
Link to Publisher's Edition
ISSN (print)
13674803
ISSN (electronic)
14602059
Recommended Citation
Liu, Chi-Man, Thomas Wong, Edward Wu, Ruibang Luo, Siu-Ming Yiu, Yingrui Li, Bingqiang Wang, Chang Yu, Xiaowen Chu, Kaiyong Zhao, Ruiqiang Li, and Tak-Wah Lam. "SOAP3: Ultra-fast GPU-based parallel alignment tool for short reads." Bioinformatics 28.6 (2012): 878-879.