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

Ruibang Luo, Thomas Wong, Jianqiao Zhu, Chi Man Liu, Xiaoqian Zhu, Edward Wu, Lap Kei Lee, Haoxiang Lin, Wenjuan Zhu, David W. Cheung, Hing Fung Ting, Siu Ming Yiu, Shaoliang Peng, Chang Yu, Yingrui Li*, Ruiqiang Li, Tak Wah Lam

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    102 Citations (Scopus)

    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.

    Original languageEnglish
    Article numbere65632
    JournalPLoS ONE
    Volume8
    Issue number5
    DOIs
    Publication statusPublished - 31 May 2013

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