Genome Assembler for Repetitive Sequences

  • Robert M. Nowak
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7339)


The article presents a new algorithm for random DNA fragment assembly. The algorithm uses an extended de Bruijn graph that stores information of reads coverage. It is able to reconstruct consecutive repetitive sequences longer than reads and to process large amount of data provided by new generation sequencers. Preliminary simulation results show the advantages of the method.


Repetitive Sequence Hamiltonian Path Simple Path Graph Dimension Assembly Algorithm 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Shendure, J., Ji, H.: Next-generation dna sequencing. Nature Biotechnology 26(10), 1135–1145 (2008)PubMedCrossRefGoogle Scholar
  2. 2.
    Sanger, F., Nicklen, S., Coulson, A.: Dna sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences 74(12), 5463 (1977)CrossRefGoogle Scholar
  3. 3.
    Lander, E., Waterman, M.: Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics 2(3), 231–239 (1988)PubMedCrossRefGoogle Scholar
  4. 4.
    Zhang, W., Chen, J., Yang, Y., Tang, Y., Shang, J., Shen, B.: A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies. PloS One 6(3), e17915 (2011)Google Scholar
  5. 5.
    Pevzner, P., Tang, H., Waterman, M.: An eulerian path approach to dna fragment assembly. Proceedings of the National Academy of Sciences 98(17), 9748 (2001)CrossRefGoogle Scholar
  6. 6.
    Myers, E.: Toward simplifying and accurately formulating fragment assembly. Journal of Computational Biology 2(2), 275–290 (1995)PubMedCrossRefGoogle Scholar
  7. 7.
    Myers, E.: The fragment assembly string graph. Bioinformatics 21(suppl. 2), ii79–ii85 (2005)Google Scholar
  8. 8.
    Pevzner, P., Tang, H., Tesler, G.: De novo repeat classification and fragment assembly. Genome Research 14(9), 1786–1796 (2004)PubMedCrossRefGoogle Scholar
  9. 9.
    Cormen, T., Leiserson, C., Rivest, R., Stein, C.: Introduction to algorithms. The MIT press (2001)Google Scholar
  10. 10.
    libraries, B.:
  11. 11.
    Hochhut, B., Wilde, C., Balling, G., Middendorf, B., Dobrindt, U., Brzuszkiewicz, E., Gottschalk, G., Carniel, E., Hacker, J.: Role of pathogenicity island-associated integrases in the genome plasticity of uropathogenic escherichia coli strain 536. Molecular Microbiology 61(3), 584–595 (2006)PubMedCrossRefGoogle Scholar
  12. 12.
    Goffeau, A., Barrell, B., Bussey, H., Davis, R., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J., Jacq, C., Johnston, M., et al.: Life with 6000 genes. Science 274(5287), 546 (1996)PubMedCrossRefGoogle Scholar
  13. 13.
    Paszkiewicz, K., Studholme, D.: De novo assembly of short sequence reads. Briefings in Bioinformatics 11(5), 457 (2010)PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Robert M. Nowak
    • 1
  1. 1.Electronics Systems InstituteWarsaw University of TechnologyWarsawPoland

Personalised recommendations