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

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 and Lam, Tak-Wah (2013) SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner. PLoS ONE, 8 5: . doi:10.1371/journal.pone.0065632

Author 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
Title SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner
Journal name PLoS ONE   Check publisher's open access policy
ISSN 1932-6203
Publication date 2013-05-31
Sub-type Article (original research)
DOI 10.1371/journal.pone.0065632
Open Access Status DOI
Volume 8
Issue 5
Total pages 11
Place of publication San Francisco, United States
Publisher Public Library of Science
Language eng
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.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Institute for Molecular Bioscience - Publications
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Citation counts: TR Web of Science Citation Count  Cited 22 times in Thomson Reuters Web of Science Article | Citations
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