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International Journal of Genomics
Volume 2017 (2017), Article ID 6120980, 12 pages
https://doi.org/10.1155/2017/6120980
Research Article

HaVec: An Efficient de Bruijn Graph Construction Algorithm for Genome Assembly

Department of CSE, BUET, ECE Building West Palasi, Dhaka 1205, Bangladesh

Correspondence should be addressed to M. Sohel Rahman

Received 9 April 2017; Revised 19 July 2017; Accepted 26 July 2017; Published 27 August 2017

Academic Editor: Brian Wigdahl

Copyright © 2017 Md Mahfuzer Rahman et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. E. Drezen, G. Rizk, R. Chikhi et al., “Gatb: genome assembly & analysis tool box,” Bioinformatics, vol. 30, no. 20, pp. 2959–2961, 2014. View at Publisher · View at Google Scholar · View at Scopus
  2. K. Zhao, W. Liu, G. Voss, and W. Muller-Wittig, “A dynamic hashing approach to build the de Bruijn graph for genome assembly,” in TENCON 2013-2013 IEEE Region 10 Conference (31194), pp. 1–4, Xi’an, China, 2013. View at Publisher · View at Google Scholar · View at Scopus
  3. R. Li, H. Zhu, J. Ruan et al., “De novo assembly of human genomes with massively parallel short read sequencing,” Genome Research, vol. 20, no. 2, pp. 265–272, 2010. View at Publisher · View at Google Scholar · View at Scopus
  4. J. T. Simpson, K. Wong, S. D. Jackman, J. E. Schein, S. J. Jones, and I. Birol, “Abyss: a parallel assembler for short read sequence data,” Genome Research, vol. 19, no. 6, pp. 1117–1123, 2009. View at Publisher · View at Google Scholar · View at Scopus
  5. T. C. Conway and A. J. Bromage, “Succinct data structures for assembling large genomes,” Bioinformatics, vol. 27, no. 4, pp. 479–486, 2011. View at Publisher · View at Google Scholar · View at Scopus
  6. C. Ye, Z. S. Ma, C. H. Cannon, M. Pop, and D. W. Yu, “Exploiting sparseness in de novo genome assembly,” BMC Bioinformatics, vol. 13, Supplement 6, p. S1, 2012. View at Publisher · View at Google Scholar
  7. J. Pell, A. Hintze, R. Canino-Koning, A. Howe, J. M. Tiedje, and C. T. Brown, “Scaling metagenome sequence assembly with probabilistic de Bruijn graphs,” Proceedings of the National Academy of Sciences, vol. 109, no. 33, pp. 13272–13277, 2012. View at Publisher · View at Google Scholar · View at Scopus
  8. R. Chikhi and G. Rizk, “Space-efficient and exact de Bruijn graph representation based on a bloom filter,” Algorithms for Molecular Biology, vol. 8, p. 22, 2013. View at Publisher · View at Google Scholar · View at Scopus
  9. M. L. Rahman, R. Sharker, S. Biswas, and M. Sohel Rahman, “Efficient de Bruijn graph construction for genome assembly using a hash table and auxiliary vector data structures,” in 2014 17th International Conference on Computer and Information Technology (ICCIT), pp. 121–126, Dhaka, Bangladesh, 2014. View at Publisher · View at Google Scholar · View at Scopus
  10. D. R. Zerbino and E. Birney, “Velvet: algorithms for de novo short read assembly using de Bruijn graphs,” Genome Research, vol. 18, no. 5, pp. 821–829, 2008. View at Publisher · View at Google Scholar · View at Scopus
  11. A. Bankevich, S. Nurk, D. Antipov et al., “Spades: a new genome assembly algorithm and its applications to single-cell sequencing,” Journal of Computational Biology, vol. 19, no. 5, pp. 455–477, 2012. View at Publisher · View at Google Scholar · View at Scopus
  12. G. Marçais and C. Kingsford, “A fast, lock-free approach for efficient parallel counting of occurrences of k-mers,” Bioinformatics, vol. 27, no. 6, pp. 764–770, 2011. View at Publisher · View at Google Scholar · View at Scopus
  13. E. Georganas, A. Buluç, J. Chapman, L. Oliker, D. Rokhsar, and K. Yelick, “Parallel de Bruijn graph construction and traversal for de novo genome assembly,” in SC14: International Conference For High Performance Computing, Networking, Storage and Analysis, pp. 437–448, New Orleans, LA, USA, 2014. View at Publisher · View at Google Scholar · View at Scopus