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IFIP International Conference on Network and Parallel Computing

NPC 2012: Network and Parallel Computing pp 145–155Cite as

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Small World Asynchronous Parallel Model for Genome Assembly

Small World Asynchronous Parallel Model for Genome Assembly

  • Jintao Meng20,21,23,
  • Jianrui Yuan21,22,
  • Jiefeng Cheng21,
  • Yanjie Wei21 &
  • …
  • Shengzhong Feng21 
  • Conference paper
  • 2339 Accesses

  • 10 Citations

Part of the Lecture Notes in Computer Science book series (LNTCS,volume 7513)

Abstract

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 genome assembly. 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, an assembler 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.

Keywords

  • parallel computing
  • De Bruijn graph
  • genome assembly

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Author information

Authors and Affiliations

  1. Institute of Computing Technology, CAS, Beijing, 100190, P.R. China

    Jintao Meng

  2. Shenzhen Institutes of Advanced Technology, CAS, Shenzhen, 518055, P.R. China

    Jintao Meng, Jianrui Yuan, Jiefeng Cheng, Yanjie Wei & Shengzhong Feng

  3. Central South University, Changsha, 410083, P.R. China

    Jianrui Yuan

  4. Graduate University of Chinese Academy of Sciences, Beijing, 100049, China

    Jintao Meng

Authors
  1. Jintao Meng
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  2. Jianrui Yuan
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  3. Jiefeng Cheng
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  4. Yanjie Wei
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  5. Shengzhong Feng
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Editor information

Editors and Affiliations

  1. Department of Computer Science and Engineering, SeoulTech, 172 Gongreung 2-dong, Nowon-gu, 139-743, Seoul, Korea

    James J. Park

  2. School of Information Technologies, The University of Sydney, Building J12, 2006, Sydney, NSW, Australia

    Albert Zomaya

  3. Division of Computer Engineering, Mokwon University, 88 Do-An-Buk-Ro, Seo-gu, 302-729, Daejeon, Korea

    Sang-Soo Yeo

  4. Department of Computer and Information Science and Engineering, University of Florida, CSE 301, 32611, Gainesville, FL, USA

    Sartaj Sahni

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© 2012 IFIP International Federation for Information Processing

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Cite this paper

Meng, J., Yuan, J., Cheng, J., Wei, Y., Feng, S. (2012). Small World Asynchronous Parallel Model for Genome Assembly. In: Park, J.J., Zomaya, A., Yeo, SS., Sahni, S. (eds) Network and Parallel Computing. NPC 2012. Lecture Notes in Computer Science, vol 7513. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-35606-3_17

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  • DOI: https://doi.org/10.1007/978-3-642-35606-3_17

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  • Print ISBN: 978-3-642-35605-6

  • Online ISBN: 978-3-642-35606-3

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