By a News Reporter-Staff News Editor at Biotech Business Week -- A new study on Life Science Research is now available. According to news reporting originating from Hong Kong, People's Republic of China, by NewsRx correspondents, research stated, "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."
Our news editors obtained a quote from the research from the University of Hong Kong, "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."
According to the news editors, the research concluded: "SOAP3-dp has been deployed on Amazon-EC2, NIH-Biowulf and Tianhe-1A."
For more information on this research see: SOAP3-dp: fast, accurate and sensitive GPU-based short read aligner. Plos One, 2013;8(5):e65632. (Public Library of Science - www.plos.org; Plos One - www.plosone.org)
The news editors report that additional information may be obtained by contacting R. Luo, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory & Dept. of Computer Science, University of Hong Kong, Hong Kong, People's Taiwan. Additional authors for this research include T. Wong, J. Zhu, C.M. Liu, X. Zhu, E. Wu, L.K. Lee, H. Lin, W. Zhu, D.W. Cheung, H.F. Ting, S.M. Yiu, S. Peng, C. Yu, Y. Li, R. Li and T.W Lam (see also Life Science Research).
Keywords for this news article include: Asia, Hong Kong, Life Science Research, People's Republic of China.
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