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

• Published in: Bioinformatics (Oxford, England) Vol. 28; no. 6; pp. 878 - 879
• Main Authors: 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
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 15.03.2012
• Subjects: Biological and medical sciences; Fundamental and applied biological sciences. Psychology; General aspects; Genome, Human; High-Throughput Nucleotide Sequencing; Humans; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Sequence Alignment - methods; Sequence Analysis, DNA - methods; Software
• ISSN: 1367-4803; 1367-4811; 1367-4811
• DOI: 10.1093/bioinformatics/bts061

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. Availability: SOAP3 is available at: http://www.cs.hku.hk/2bwt-tools/soap3; http://soap.genomics.org.cn/soap3.html. Contact:  liruiqiang@gmail.com, twlam@cs.hku.hk