Fast GPU Read Alignmennt with Burrows Wheeler Transform Based Index
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概要
- 論文の詳細を見る
This paper addresses the problem of performing faster read alignment on GPU devices. The computationally-intensive task of DNA sequence processing is approached from the perspective of parallel computation. We found memory limitations to be one of the biggest performance issues, and attempted to decrease memory footprint of alignment algorithm to boost GPU performance. Suggested implementation uses index based on Burrows-Wheeler transform and shows 3-4 time speed improvement over the previous fastest solution.
- 2011-07-20
著者
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Satoshi Matsuoka
Tokyo Institute of Technology
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Naoya Maruyama
Tokyo Institute of Technology
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Satoshi Matsuoka
Tokyo Institute Of Technology|national Institute Of Informatics|japan Science And Technology Agency
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Satoshi Matsuoka
National Inst. Of Informatics
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Aleksandr Drozd
Tokyo Institute Of Technology
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