Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

How to apply de Bruijn graphs to genome assembly

A mathematical concept known as a de Bruijn graph turns the formidable challenge of assembling a contiguous genome from billions of short sequencing reads into a tractable computational problem.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type



Prices may be subject to local taxes which are calculated during checkout

Figure 1: Bridges of Königsberg problem.
Figure 2: De Bruijn graph.
Figure 3: Two strategies for genome assembly: from Hamiltonian cycles to Eulerian cycles.

Similar content being viewed by others


  1. Euler, L. Commentarii Academiae Scientiarum Petropolitanae 8, 128–140 (1741).

    Google Scholar 

  2. Skiena, S. The Algorithm Design Manual (Springer, Berlin, 2008).

    Book  Google Scholar 

  3. Lander, E. et al. Nature 409, 860–921 (2001).

    Article  CAS  Google Scholar 

  4. Venter, J.C. et al. Science 291, 1304–1351 (2001).

    Article  CAS  Google Scholar 

  5. Kececioglu, J. & Myers, E. Algorithmica 13, 7–51 (1995).

    Article  Google Scholar 

  6. Adams, M. et al. Science 287, 2185–2195 (2000).

    Article  Google Scholar 

  7. Fleischmann, R. et al. Science 269, 496–512 (1995).

    Article  CAS  Google Scholar 

  8. Schatz, M., Delcher, A. & Salzberg, S. Genome Res. 20, 1165–1173 (2010).

    Article  CAS  Google Scholar 

  9. Bandeira, N., Pham, V., Pevzner, P., Arnott, D. & Lill, J. Nat. Biotechnol. 26, 1336–1338 (2008).

    Article  CAS  Google Scholar 

  10. Pham, S. & Pevzner, P.A. Bioinformatics 26, 2509–2516 (2010).

    Article  CAS  Google Scholar 

  11. Grabherr, M. et al. Nat. Biotechnol. 29, 644–652 (2011).

    Article  CAS  Google Scholar 

  12. de Bruijn, N. Proc. Nederl. Akad. Wetensch. 49, 758–764 (1946).

    Google Scholar 

  13. Idury, R. & Waterman, M. J. Comput. Biol. 2, 291–306 (1995).

    Article  CAS  Google Scholar 

  14. Pevzner, P.A., Tang, H. & Waterman, M. Proc. Natl. Acad. Sci. USA 98, 9748–9753 (2001).

    Article  CAS  Google Scholar 

  15. Pevzner, P.A., Tang, H. & Tesler, G. Genome Res. 14, 1786–1796 (2004).

    Article  CAS  Google Scholar 

  16. Chaisson, M. & Pevzner, P.A. Genome Res. 18, 324–330 (2008).

    Article  CAS  Google Scholar 

  17. Zerbino, D. & Birney, E. Genome Res. 18, 821–829 (2008).

    Article  CAS  Google Scholar 

  18. Butler, J. et al. Genome Res. 18, 810–820 (2008).

    Article  CAS  Google Scholar 

  19. Simpson, J. et al. Genome Res. 19, 1117–1123 (2009).

    Article  CAS  Google Scholar 

  20. Li, R. et al. Genome Res. 20, 265–272 (2010).

    Article  CAS  Google Scholar 

  21. Paszkiewicz, K. & Studholme, D. Brief. Bioinform. 11, 457–472 (2010).

    Article  CAS  Google Scholar 

  22. Miller, J., Koren, S. & Sutton, G. Genomics 95, 315–327 (2010).

    Article  CAS  Google Scholar 

  23. Drmanac, R., Labat, I., Brukner, I. & Crkvenjakov, R. Genomics 4, 114–128 (1989).

    Article  CAS  Google Scholar 

  24. Southern, E. United Kingdom patent application gb8810400 (1988).

  25. Lysov, Y. et al. Doklady Academy Nauk USSR 303, 1508–1511 (1988).

    CAS  Google Scholar 

  26. Pevzner, P.A. J. Biomol. Struct. Dyn. 7, 63–73 (1989).

    Article  CAS  Google Scholar 

Download references


This work was supported by grants from Howard Hughes Medical Institute (HHMI grant 52005726), the US National Institutes of Health (NIH grant 3P41RR024851-02S1) and the National Science Foundation (NSF grant DMS-0718810). We are grateful to S. Wasserman for many helpful comments.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Pavel A Pevzner.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Figure 1 and 2

De Bruijn graph from reads with sequencing errors (PDF 139 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Compeau, P., Pevzner, P. & Tesler, G. How to apply de Bruijn graphs to genome assembly. Nat Biotechnol 29, 987–991 (2011).

Download citation

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research