| Presentation | 2014-06-12 Highly-Parallel FPGA Accelerator for DNA Sequence Alignment Using the Burrows-Wheeler Algorithm Hasitha Muthumala WAIDYASOORIYA, Masanori HARIYAMA, Michitaka KAMEYAMA, |
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| PDF Download Page |  PDF download Page Link |
| Abstract(in Japanese) | (See Japanese page) |
| Abstract(in English) | The mapping of millions of short DNA fragments to a large genome is a very important aspect of the modern bioinformatics. However, software-based DNA sequence mapping takes many days to complete. This paper proposes an FPGA-based hardware accelerator to increase the mapping speed. Proposed accelerator maps over hundred short DNA fragments simultaneously. We apply a data encoding scheme that reduces the genome data size to just 4%, and propose a hardware decoder to decode the data in single clock cycle. We also design customized data paths to increase the speed for random data access. According to the experimental results, the speed-up of the proposed architecture is 15 times compared to its equivalent software application. |
| Keyword(in Japanese) | (See Japanese page) |
| Keyword(in English) | Short-read mapping / FPGA / Human DNA mapping |
| Paper # | RECONF2014-4 |
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| Conference Information | |
| Committee | RECONF |
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| Conference Date | 2014/6/4(1days) |
| Place (in Japanese) | (See Japanese page) |
| Place (in English) | |
| Topics (in Japanese) | (See Japanese page) |
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| Paper Information | |
| Registration To | Reconfigurable Systems (RECONF) |
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| Language | JPN |
| Title (in Japanese) | (See Japanese page) |
| Sub Title (in Japanese) | (See Japanese page) |
| Title (in English) | Highly-Parallel FPGA Accelerator for DNA Sequence Alignment Using the Burrows-Wheeler Algorithm |
| Sub Title (in English) | |
| Keyword(1) | Short-read mapping |
| Keyword(2) | FPGA |
| Keyword(3) | Human DNA mapping |
| 1st Author's Name | Hasitha Muthumala WAIDYASOORIYA |
| 1st Author's Affiliation | Graduate School of Information Sciences, Tohoku University() |
| 2nd Author's Name | Masanori HARIYAMA |
| 2nd Author's Affiliation | Graduate School of Information Sciences, Tohoku University |
| 3rd Author's Name | Michitaka KAMEYAMA |
| 3rd Author's Affiliation | Graduate School of Information Sciences, Tohoku University |
| Date | 2014-06-12 |
| Paper # | RECONF2014-4 |
| Volume (vol) | vol.114 |
| Number (no) | 75 |
| Page | pp.pp.- |
| #Pages | 4 |
| Date of Issue | |