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 language | English (US) |
|---|---|
| Pages (from-to) | 336-352 |
| Number of pages | 17 |
| Journal | Journal of Computational Biology |
| Volume | 22 |
| Issue number | 5 |
| DOIs | |
| State | Published - May 1 2015 |
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All Science Journal Classification (ASJC) codes
- Modeling and Simulation
- Molecular Biology
- Genetics
- Computational Mathematics
- Computational Theory and Mathematics
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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 journal › Article
TY - JOUR
T1 - On the representation of de bruijn graphs
AU - Chikhi, Rayan
AU - Limasset, Antoine
AU - Jackman, Shaun
AU - Simpson, Jared T.
AU - Medvedev, Paul
PY - 2015/5/1
Y1 - 2015/5/1
N2 - 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.
AB - 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.
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UR - http://www.scopus.com/inward/citedby.url?scp=84929660696&partnerID=8YFLogxK
U2 - 10.1089/cmb.2014.0160
DO - 10.1089/cmb.2014.0160
M3 - Article
C2 - 25629448
AN - SCOPUS:84929660696
VL - 22
SP - 336
EP - 352
JO - Journal of Computational Biology
JF - Journal of Computational Biology
SN - 1066-5277
IS - 5
ER -