| Small world asynchronous parallel model for genome assembly | |
| Meng jintao; Yuan jianrui; Cheng jiefeng; Wei yanjie; Feng shengzhong | |
| 2012 | |
| 会议名称 | 9th IFIP International Conference, NPC 2012 |
| 会议地点 | Gwangju, Korea |
| 英文摘要 | Large de bruijn graph based algorithm is widely used in genome assembly and metagenetic assembly. The scale of this kind of graphs - in some cases billions of vertices and edges - poses challenges to genome assembly problem. In this paper, a one-step bi-directed graph is used to abstract the problem of genomeassembly. After that small world asynchronous parallel model (SWAP) is proposed to handle the edge merging operation predefined in the graph. SWAP aims at making use of the locality of computing and communication to explore parallelism for graph algorithm. Based on the above graph abstraction and SWAP model, anassembler is developed, and experiment results shows that a factor of 20 times speedup is achieved when the number of processors scales from 10 to 640 when testing on processing C.elegans data. © IFIP International Federation for Information Processing 2012.(23 refs) |
| 收录类别 | EI |
| 语种 | 英语 |
| 内容类型 | 会议论文 |
| 源URL | [http://ir.siat.ac.cn:8080/handle/172644/4223]  |
| 专题 | 深圳先进技术研究院_数字所 |
| 作者单位 | 2012 |
| 推荐引用方式 GB/T 7714 | Meng jintao,Yuan jianrui,Cheng jiefeng,et al. Small world asynchronous parallel model for genome assembly[C]. 见:9th IFIP International Conference, NPC 2012. Gwangju, Korea. |
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