title: SOAP3: ultra-fast GPU-based parallel alignment tool for short reads.
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.
authors.affiliation: Department of Computer Science, The University of Hong Kong, Hong Kong, China.
authors.forename: Chi-Man
authors.initials: CM
authors.lastname: Liu
authors.forename: Thomas
authors.initials: T
authors.lastname: Wong
authors.forename: Edward
authors.initials: E
authors.lastname: Wu
authors.forename: Ruibang
authors.initials: R
authors.lastname: Luo
authors.forename: Siu-Ming
authors.initials: SM
authors.lastname: Yiu
authors.forename: Yingrui
authors.initials: Y
authors.lastname: Li
authors.forename: Bingqiang
authors.initials: B
authors.lastname: Wang
authors.forename: Chang
authors.initials: C
authors.lastname: Yu
authors.forename: Xiaowen
authors.initials: X
authors.lastname: Chu
authors.forename: Kaiyong
authors.initials: K
authors.lastname: Zhao
authors.forename: Ruiqiang
authors.initials: R
authors.lastname: Li
authors.forename: Tak-Wah
authors.initials: TW
authors.lastname: Lam
mesh_terms: D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software