title: SOAP3-dp: fast, accurate and sensitive GPU-based short read aligner.
abstract: To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, CUSHAW2, GEM and GPU-based aligners BarraCUDA and CUSHAW, SOAP3-dp was found to be two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate (FDR) on Illumina reads with different lengths. Transcending its predecessor SOAP3, which does not allow gapped alignment, SOAP3-dp by default tolerates alignment similarity as low as 60%. Real data evaluation using human genome demonstrates SOAP3-dp's power to enable more authentic variants and longer Indels to be discovered. Fosmid sequencing shows a 9.1% FDR on newly discovered deletions. SOAP3-dp natively supports BAM file format and provides the same scoring scheme as BWA, which enables it to be integrated into existing analysis pipelines. SOAP3-dp has been deployed on Amazon-EC2, NIH-Biowulf and Tianhe-1A.
authors.affiliation: HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory & Department of Computer Science, University of Hong Kong, Hong Kong, China.
authors.forename: Ruibang
authors.initials: R
authors.lastname: Luo
authors.forename: Thomas
authors.initials: T
authors.lastname: Wong
authors.forename: Jianqiao
authors.initials: J
authors.lastname: Zhu
authors.forename: Chi-Man
authors.initials: CM
authors.lastname: Liu
authors.forename: Xiaoqian
authors.initials: X
authors.lastname: Zhu
authors.forename: Edward
authors.initials: E
authors.lastname: Wu
authors.forename: Lap-Kei
authors.initials: LK
authors.lastname: Lee
authors.forename: Haoxiang
authors.initials: H
authors.lastname: Lin
authors.forename: Wenjuan
authors.initials: W
authors.lastname: Zhu
authors.forename: David W
authors.initials: DW
authors.lastname: Cheung
authors.forename: Hing-Fung
authors.initials: HF
authors.lastname: Ting
authors.forename: Siu-Ming
authors.initials: SM
authors.lastname: Yiu
authors.forename: Shaoliang
authors.initials: S
authors.lastname: Peng
authors.forename: Chang
authors.initials: C
authors.lastname: Yu
authors.forename: Yingrui
authors.initials: Y
authors.lastname: Li
authors.forename: Ruiqiang
authors.initials: R
authors.lastname: Li
authors.forename: Tak-Wah
authors.initials: TW
authors.lastname: Lam
mesh_terms: D019295:Computational Biology / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D057188:Workflow