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

doi:10.1093/bioinformatics/bts061

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	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 ; Lam, Tak-Wah
刊名	bioinformatics
	2012
关键词	GENOME
DOI	10.1093/bioinformatics/bts061
英文摘要	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.; Biochemical Research Methods; Biotechnology & Applied Microbiology; Computer Science, Interdisciplinary Applications; Mathematical & Computational Biology; Statistics & Probability; SCI(E); 0; ARTICLE; 6; 878-879; 28
语种	英语
内容类型	期刊论文
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/393563]
专题	生命科学学院
推荐引用方式 GB/T 7714	Liu, Chi-Man,Wong, Thomas,Wu, Edward,et al. SOAP3: ultra-fast GPU-based parallel alignment tool for short reads[J]. bioinformatics,2012.
APA	Liu, Chi-Man.,Wong, Thomas.,Wu, Edward.,Luo, Ruibang.,Yiu, Siu-Ming.,...&Lam, Tak-Wah.(2012).SOAP3: ultra-fast GPU-based parallel alignment tool for short reads.bioinformatics.
MLA	Liu, Chi-Man,et al."SOAP3: ultra-fast GPU-based parallel alignment tool for short reads".bioinformatics (2012).