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

被引：154

作者：

Liu, Chi-Man ^{[3
]}

Wong, Thomas ^{[3
]}

Wu, Edward ^{[3
]}

Luo, Ruibang ^{[3
]}

Yiu, Siu-Ming ^{[3
]}

Li, Yingrui ^{[4
]}

Wang, Bingqiang ^{[4
]}

Yu, Chang ^{[4
]}

Chu, Xiaowen ^{[5
]}

Zhao, Kaiyong ^{[5
]}

Li, Ruiqiang ^{[1
,2
]}

Lam, Tak-Wah ^{[3
]}

机构：

[1] Peking Univ, Peking Tsinghua Ctr Life Sci, Biodynam Opt Imaging Ctr, Beijing 100871, Peoples R China

[2] Peking Univ, Sch Life Sci, Beijing 100871, Peoples R China

[3] Univ Hong Kong, Dept Comp Sci, Hong Kong, Hong Kong, Peoples R China

[4] BGI Shenzhen, Shenzhen, Peoples R China

[5] Hong Kong Baptist Univ, Dept Comp Sci, Hong Kong, Hong Kong, Peoples R China

来源：

BIOINFORMATICS | 2012年 / 28卷 / 06期

关键词：

GENOME;

D O I：

10.1093/bioinformatics/bts061

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

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.

引用

页码：878 / 879

页数：2

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