| Presentation | 2013/6/20 Evaluation of Sparse k-mer graph algorithm and its implementation on Velvet SHUNSUKE YOSHIKAWA, TAKASHI ISHIDA, MASAKAZU SEKIJIMA, YUTAKA AKIYAMA, |
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| PDF Download Page | PDF download Page Link |
| Abstract(in Japanese) | (See Japanese page) |
| Abstract(in English) | Development of Next Generation Sequencing technologies has provided an unprecedented increase in DNA sequencing throuput while this technology produces shorter reads than previous technology. These two factors make a number of new short read de novo assemblers. In this report, by evaluation of Sparse Assembler, we clarified that this asssembler is useful at the point of memory usage and time, while producing less quality of contigs than other assemblers already developed. This study was made to assembly with less computer memory and in shorter time than previous study by implement Sparse k-mer graph algorithm on Velvet, which is the most widely used assembler. |
| Keyword(in Japanese) | (See Japanese page) |
| Keyword(in English) | Next Generartion Sequencing / de novo assembly / Velvet / Sparse Assembler |
| Paper # | Vol.2013-BIO-34 No.1 |
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| Conference Information | |
| Committee | NC |
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| Conference Date | 2013/6/20(1days) |
| Place (in Japanese) | (See Japanese page) |
| Place (in English) | |
| Topics (in Japanese) | (See Japanese page) |
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| Vice Chair | |
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| Paper Information | |
| Registration To | Neurocomputing (NC) |
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| Language | JPN |
| Title (in Japanese) | (See Japanese page) |
| Sub Title (in Japanese) | (See Japanese page) |
| Title (in English) | Evaluation of Sparse k-mer graph algorithm and its implementation on Velvet |
| Sub Title (in English) | |
| Keyword(1) | Next Generartion Sequencing |
| Keyword(2) | de novo assembly |
| Keyword(3) | Velvet |
| Keyword(4) | Sparse Assembler |
| 1st Author's Name | SHUNSUKE YOSHIKAWA |
| 1st Author's Affiliation | Department of Computer Science, Graduate school of Information Science and Engineering, Tokyo Institute of Technology() |
| 2nd Author's Name | TAKASHI ISHIDA |
| 2nd Author's Affiliation | Department of Computer Science, Graduate school of Information Science and Engineering, Tokyo Institute of Technology |
| 3rd Author's Name | MASAKAZU SEKIJIMA |
| 3rd Author's Affiliation | Department of Computer Science, Graduate school of Information Science and Engineering, Tokyo Institute of Technology:Global Scientific Information and Computing Center, Tokyo Institute of Technology |
| 4th Author's Name | YUTAKA AKIYAMA |
| 4th Author's Affiliation | Department of Computer Science, Graduate school of Information Science and Engineering, Tokyo Institute of Technology |
| Date | 2013/6/20 |
| Paper # | Vol.2013-BIO-34 No.1 |
| Volume (vol) | vol.113 |
| Number (no) | 111 |
| Page | pp.pp.- |
| #Pages | 7 |
| Date of Issue | |