On the representation of de bruijn graphs

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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

39 Scopus citations

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.

Original languageEnglish (US)
Title of host publicationResearch in Computational Molecular Biology - 18th Annual International Conference, RECOMB 2014, Proceedings
PublisherSpringer Verlag
Pages35-55
Number of pages21
ISBN (Print)9783319052687
DOIs
StatePublished - Jan 1 2014
Event18th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2014 - Pittsburgh, PA, United States
Duration: Apr 2 2014Apr 5 2014

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume8394 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other18th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2014
CountryUnited States
CityPittsburgh, PA
Period4/2/144/5/14

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

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    Chikhi, R., Limasset, A., Jackman, S., Simpson, J. T., & Medvedev, P. (2014). On the representation of de bruijn graphs. In Research in Computational Molecular Biology - 18th Annual International Conference, RECOMB 2014, Proceedings (pp. 35-55). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 8394 LNBI). Springer Verlag. https://doi.org/10.1007/978-3-319-05269-4_4