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On the Representation of de Bruijn Graphs

  • Conference paper
Research in Computational Molecular Biology (RECOMB 2014)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 8394))

Abstract

The de Bruijn graph plays an important role in bioinformatics, especially in the context of de novo assembly. However, the representation of the de Bruijn graph in memory is a computational bottleneck for many assemblers. Recent papers proposed a navigational data structure approach in order to improve memory usage. We prove several theoretical space lower bounds to show the limitations of these types of approaches. We further design and implement a general data structure (dbgfm) and demonstrate its use on a human whole-genome dataset, achieving space usage of 1.5 GB and a 46% improvement over previous approaches. As part of dbgfm, we develop the notion of frequency-based minimizers and show how it can be used to enumerate all maximal simple paths of the de Bruijn graph using only 43 MB of memory. Finally, we demonstrate that our approach can be integrated into an existing assembler by modifying the ABySS software to use dbgfm.

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Author information

Authors and Affiliations

  1. Department of Computer Science and Engineering, The Pennsylvania State University, USA

    Rayan Chikhi & Paul Medvedev

  2. ENS Cachan Brittany, Bruz, France

    Antoine Limasset

  3. Canada’s Michael Smith Genome Sciences Centre, Canada

    Shaun Jackman

  4. Ontario Institute for Cancer Research, Toronto, Canada

    Jared T. Simpson

  5. Department of Biochemistry and Molecular Biology, The Pennsylvania State University, USA

    Paul Medvedev

  6. Genomics Institute of the Huck Institutes of the Life Sciences, The Pennsylvania State University, USA

    Paul Medvedev

Authors
  1. Rayan Chikhi
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  2. Antoine Limasset
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  3. Shaun Jackman
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  4. Jared T. Simpson
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  5. Paul Medvedev
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Editor information

Editors and Affiliations

  1. School of Computer Science, Tel Aviv University, 69978, Tel Aviv, Israel

    Roded Sharan

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© 2014 Springer International Publishing Switzerland

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Chikhi, R., Limasset, A., Jackman, S., Simpson, J.T., Medvedev, P. (2014). On the Representation of de Bruijn Graphs. In: Sharan, R. (eds) Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science(), vol 8394. Springer, Cham. https://doi.org/10.1007/978-3-319-05269-4_4

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  • DOI: https://doi.org/10.1007/978-3-319-05269-4_4

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-05268-7

  • Online ISBN: 978-3-319-05269-4

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