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IFIP International Conference on Network and Parallel Computing

NPC 2012: Network and Parallel Computing pp 14–21Cite as

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DGraph: Algorithms for Shortgun Reads Assembly Using De Bruijn Graph

DGraph: Algorithms for Shortgun Reads Assembly Using De Bruijn Graph

  • Jintao Meng20,21,23,
  • Jianrui Yuan21,22,
  • Jiefeng Cheng21,
  • Yanjie Wei21 &
  • …
  • Shengzhong Feng21 
  • Conference paper
  • 2345 Accesses

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

Abstract

Massively parallel DNA sequencing platforms have become widely available, reducing the cost of DNA sequencing by over two orders of magnitude, and democratizing the field by putting the sequencing capacity of a major genome center in the hands of individual investigators. New challenges include the development of robust protocols for generating sequencing libraries, building effective new approaches to resequence and data-analysis. In this paper we demonstrate a new sequencing algorithm, named DGraph, which has two modules, one module is responsible to construct De Bruijn graph by cutting reads into k-mers, and the other’s duty is to simplify this graph and collect all long contigs. The authors didn’t adapt the sequence graph reductions operations proposed by RAMANA M.IDURY or Finding Eulerian Superpaths proved by Pavel A.Pevzner or bubble remove steps suggested by Danial Zerbino, As the first operations was computing expensive, and the second one was impractical, and the last one did not benefit either the quality of contigs or the efficiency of the assembler. Our assembler was focused only on efficient and effective error removal and path reduction operations. Applying DGraph to the simulation data of fruit fly Drosophila melanogaster chromosome X, DGraph (3min) is about six times faster than velvet 0.3 (19 mins), and its coverage (92.5%) is also better than velvet (78.2%) when k = 21. Compare to velvet, the results shows that the algorithm of DGraph is a faster program with high quality results.

Keywords

  • De Bruijn graph
  • graph algorithm
  • short read assembler

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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). DGraph: Algorithms for Shortgun Reads Assembly Using De Bruijn Graph. 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_2

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  • DOI: https://doi.org/10.1007/978-3-642-35606-3_2

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  • Print ISBN: 978-3-642-35605-6

  • Online ISBN: 978-3-642-35606-3

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