title: On the representation of de Bruijn graphs.
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.
authors: 1 Department of Computer Science and Engineering, The Pennsylvania State University , State College, Pennsylvania.
authors: Rayan
authors: R
authors: Chikhi
authors: Antoine
authors: A
authors: Limasset
authors: Shaun
authors: S
authors: Jackman
authors: Jared T
authors: JT
authors: Simpson
authors: Paul
authors: P
authors: Medvedev
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data*; D003196:Computer Graphics / Q000706:statistics & numerical data*; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D017422:Sequence Analysis, DNA / Q000706:statistics & numerical data*; D012984:Software