On the representation of de bruijn graphs

Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared T. Simpson, Paul Medvedev

Research output: Contribution to journalArticle

12 Citations (Scopus)

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 1.5GB 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 43MB of memory. Finally, we demonstrate that our approach can be integrated into an existing assembler by modifying the ABySS software to use dbgfm.

Original languageEnglish (US)
Pages (from-to)336-352
Number of pages17
JournalJournal of Computational Biology
Volume22
Issue number5
DOIs
StatePublished - May 1 2015

Fingerprint

De Bruijn Graph
Data storage equipment
Data structures
Data Structures
Human Genome
Bioinformatics
Computational Biology
Minimizer
Demonstrate
Genome
Software
Genes
Lower bound
Path

All Science Journal Classification (ASJC) codes

  • Modeling and Simulation
  • Molecular Biology
  • Genetics
  • Computational Mathematics
  • Computational Theory and Mathematics

Cite this

Chikhi, R., Limasset, A., Jackman, S., Simpson, J. T., & Medvedev, P. (2015). On the representation of de bruijn graphs. Journal of Computational Biology, 22(5), 336-352. https://doi.org/10.1089/cmb.2014.0160
Chikhi, Rayan ; Limasset, Antoine ; Jackman, Shaun ; Simpson, Jared T. ; Medvedev, Paul. / On the representation of de bruijn graphs. In: Journal of Computational Biology. 2015 ; Vol. 22, No. 5. pp. 336-352.
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Chikhi, R, Limasset, A, Jackman, S, Simpson, JT & Medvedev, P 2015, 'On the representation of de bruijn graphs', Journal of Computational Biology, vol. 22, no. 5, pp. 336-352. https://doi.org/10.1089/cmb.2014.0160

On the representation of de bruijn graphs. / Chikhi, Rayan; Limasset, Antoine; Jackman, Shaun; Simpson, Jared T.; Medvedev, Paul.

In: Journal of Computational Biology, Vol. 22, No. 5, 01.05.2015, p. 336-352.

Research output: Contribution to journalArticle

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Chikhi R, Limasset A, Jackman S, Simpson JT, Medvedev P. On the representation of de bruijn graphs. Journal of Computational Biology. 2015 May 1;22(5):336-352. https://doi.org/10.1089/cmb.2014.0160