SOAP3-dp: fast, accurate and sensitive GPU-based short read aligner

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, d...

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Bibliographic Details
Published in:PloS one 2013-05, Vol.8 (5), p.e65632
Main Authors: Luo, Ruibang, Wong, Thomas, Zhu, Jianqiao, Liu, Chi-Man, Zhu, Xiaoqian, Wu, Edward, Lee, Lap-Kei, Lin, Haoxiang, Zhu, Wenjuan, Cheung, David W, Ting, Hing-Fung, Yiu, Siu-Ming, Peng, Shaoliang, Yu, Chang, Li, Yingrui, Li, Ruiqiang, Lam, Tak-Wah
Format: Article
Language:English
Subjects:
Algorithms
Alignment
Bioinformatics
Biology
Computational Biology - methods
Computer applications
Computer Science
Deoxyribonucleic acid
DNA
Genomes
Genomics
High-Throughput Nucleotide Sequencing
Humans
Laboratories
Life sciences
Pipelining (computers)
Reproducibility of Results
Seeds
Sensitivity
Sensitivity and Specificity
Sequence Alignment - methods
Sequence Analysis, DNA - methods
Software
Workflow
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Summary: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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0065632