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How to apply de Bruijn graphs to genome assembly

Nature Biotechnology volume 29, pages 987–991 (2011)Cite this article

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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.

Problems with alignment-based assembly

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

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Acknowledgements

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.

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Authors and Affiliations

  1. Phillip E. C. Compeau and Glenn Tesler are in the Department of Mathematics, University of California San Diego, La Jolla, California, USA,

    Phillip E C Compeau & Glenn Tesler

  2. Pavel A. Pevzner is in the Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA.,

    Pavel A Pevzner

Authors
  1. Phillip E C Compeau
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  2. Pavel A Pevzner
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  3. Glenn Tesler
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Corresponding author

Correspondence to Pavel A Pevzner.

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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)

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Compeau, P., Pevzner, P. & Tesler, G. How to apply de Bruijn graphs to genome assembly. Nat Biotechnol 29, 987–991 (2011). https://doi.org/10.1038/nbt.2023

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