SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner

Ruibang Luo, Thomas Wong, Jianqiao Zhu, Chi-Man Liu, Edward Wu, Lap-Kei Lee, Haoxiang Lin, Wenjuan Zhu, David W. Cheung, Hing-Fung Ting, Siu-Ming Yiu, Chang Yu, Yingrui Li, Ruiqiang Li, Tak-Wah Lam
HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory & Department of Computer Science, University of Hong Kong, Hong Kong
arXiv:1302.5507 [q-bio.GN], (22 Feb 2013)


   author={Luo}, R. and {Wong}, T. and {Zhu}, J. and {Liu}, C.-M. and {Wu}, E. and {Lee}, L.-K. and {Lin}, H. and {Zhu}, W. and {Cheung}, D.~W. and {Ting}, H.-F. and {Yiu}, S.-M. and {Yu}, C. and {Li}, Y. and {Li}, R. and {Lam}, T.-W.},

   title={"{SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner}"},

   journal={ArXiv e-prints},




   keywords={Quantitative Biology – Genomics},




   adsnote={Provided by the SAO/NASA Astrophysics Data System}


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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, GEM and GPU-based aligners including BarraCUDA and CUSHAW, SOAP3-dp is 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 percent. 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 percent FDR on newly discovered deletions. SOAP3-dp natively supports BAM file format and provides a scoring scheme same 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.
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