Advertisement

Improved Parallel Processing of Massive De Bruijn Graph for Genome Assembly

  • Li Zeng
  • Jiefeng Cheng
  • Jintao Meng
  • Bingqiang Wang
  • Shengzhong Feng
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7808)

Abstract

De Bruijn graph is a vastly used technique for developing genome assembly software nowadays. The scale of this kind of graph can reach billions of vertices and edges which poses great challenges to the genome assembly task. It is of great importance to study scalable genome assembly algorithms in order to cope with this situation. Despite some recent works which begin to address the scalability problem with parallel assembly algorithms, massive De Bruijn graph processing is still very time consuming which needs optimized operations.  In this paper, we aim to significantly improve the efficiency of massive De Bruijn graph processing. Specifically, the time consuming and memory intensive processing are the De Bruijn graph construction phase and the simplification phase. We observe that the existing list ranking approach repeatedly performs parallel global sorting over all De Bruijn graph vertices, which results in a huge amount of communications between computing nodes. Therefore, we propose to use depth-first traversal over the underlying De Bruijn graph once to achieve the same objective as the existing list ranking approach. The new method is fast, effective and can be executed in parallel. It has a computing complexity of O(g/p) and communication complexity of O(g), which is smaller than the existing list ranking approach, here g is the length of genome reference, p is the number of processors. Our experimental results using error-free data show that, when the number of processors scales from 8 to 128, our algorithm has a speedup of 10 times on processing simulated data of Yeast and C.elegans.

Keywords

Parallelized Graph Algorithm De Bruijn Graph Genome Assembler 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Kundeti, V.K., Rajasekaran, S., Dinh, H., et al.: Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs. BMC Bioinformatics 11(560) (2010)Google Scholar
  2. 2.
    Kececioglu, J.D., Myers, E.W.: Combinatorial algorithms for DNA sequence assembly. Algorithmica 13(1), 7–51 (1995)MathSciNetzbMATHCrossRefGoogle Scholar
  3. 3.
    Pevzner, P.A., Tang, H., Waterman, M.S.: An Eulerian path approach to DNA fragment assembly. Proceedings of the National Academy of Sciences of the United States of America 98(17), 9748–9753 (2001)MathSciNetzbMATHCrossRefGoogle Scholar
  4. 4.
    Medvedev, P., Georgiou, K., Myers, G., Brudno, M.: Computability of models for sequence assembly. In: Giancarlo, R., Hannenhalli, S. (eds.) WABI 2007. LNCS (LNBI), vol. 4645, pp. 289–301. Springer, Heidelberg (2007)CrossRefGoogle Scholar
  5. 5.
    Jackson, B.G., Aluru, S.: Parallel Construction of Bidirected String Graphs for Genome Assembly, 346–353 (2008)Google Scholar
  6. 6.
    Butler, J., Maccallum, I., Kleber, M., et al.: ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res. 18(5), 810–820 (2008)CrossRefGoogle Scholar
  7. 7.
    Zerbino, D.R., Birney, E.: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18(5), 821–829 (2008)CrossRefGoogle Scholar
  8. 8.
    Peng, Y., Leung, H.C.M., Yiu, S.M., Chin, F.Y.L.: IDBA–A Practical Iterative de Bruijn Graph De Novo Assembler. In: Berger, B. (ed.) RECOMB 2010. LNCS, vol. 6044, pp. 426–440. Springer, Heidelberg (2010)CrossRefGoogle Scholar
  9. 9.
    Li, R., Zhu, H., Ruan, J., et al.: De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20(2), 265–272 (2010)CrossRefGoogle Scholar
  10. 10.
    Simpson, J.T., Wong, K., Jackman, S.D., et al.: ABySS: a parallel assembler for short read sequence data. Genome Res. 19(6), 1117–1123 (2009)CrossRefGoogle Scholar
  11. 11.
    Jackson, B., Regennitter, M., Yang, X., et al.: Parallel de novo assembly of large genomes from high-throughput short reads. IEEE (2010) Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Li Zeng
    • 1
  • Jiefeng Cheng
    • 1
  • Jintao Meng
    • 1
    • 2
    • 3
  • Bingqiang Wang
    • 4
  • Shengzhong Feng
    • 1
  1. 1.Shenzhen Institutes of Advanced TechnologyCASShenzhenP.R. China
  2. 2.Institute of Computing TechnologyCASBeijingP.R. China
  3. 3.Graduate University of Chinese Academy of SciencesBeijingChina
  4. 4.Beijing Genomics InstituteShenzhenChina

Personalised recommendations