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Efficient Construction of a Compressed de Bruijn Graph for Pan-Genome Analysis

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Book cover Combinatorial Pattern Matching (CPM 2015)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 9133))

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Abstract

Recently, Marcus et al. (Bioinformatics 2014) proposed to use a compressed de Bruijn graph of maximal exact matches to describe the relationship between the genomes of many individuals/strains of the same or closely related species. They devised an \(O(n\log g)\) time algorithm called splitMEM that constructs this graph directly (i.e., without using the uncompressed de Bruijn graph) based on a suffix tree, where \(n\) is the total length of the genomes and \(g\) is the length of the longest genome. In this paper, we present an algorithm that outperforms their algorithm in theory and in practice. More precisely, our algorithm has a better worst-case time complexity of \(O(n\log \sigma )\), where \(\sigma \) is the size of the alphabet (\(\sigma = 4\) for DNA). Moreover, experiments show that it is much faster than splitMEM while using only a fraction of the space required by splitMEM.

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Acknowledgments

This work was supported by the DFG (OH 53/6-1).

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Authors and Affiliations

  1. Institute of Theoretical Computer Science, University of Ulm, 89069, Ulm, Germany

    Timo Beller & Enno Ohlebusch

Authors
  1. Timo Beller
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  2. Enno Ohlebusch
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Correspondence to Timo Beller .

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Editors and Affiliations

  1. Department of Computer Science, University of Verona, Verona, Italy

    Ferdinando Cicalese

  2. Department of Computer Science, Bar-Ilan University, Ramat Gan, Israel

    Ely Porat

  3. Department of Computer Science, University of Salerno, Fisciano, Italy

    Ugo Vaccaro

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Beller, T., Ohlebusch, E. (2015). Efficient Construction of a Compressed de Bruijn Graph for Pan-Genome Analysis. In: Cicalese, F., Porat, E., Vaccaro, U. (eds) Combinatorial Pattern Matching. CPM 2015. Lecture Notes in Computer Science(), vol 9133. Springer, Cham. https://doi.org/10.1007/978-3-319-19929-0_4

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  • DOI: https://doi.org/10.1007/978-3-319-19929-0_4

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-19928-3

  • Online ISBN: 978-3-319-19929-0

  • eBook Packages: Computer ScienceComputer Science (R0)

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