Variable-Order de Bruijn Graphs

The de Bruijn graph GK of a set of strings Sis a key data structure in genome assembly that represents overlaps between all the K-length substrings of S. Construction and navigation of the graph is a space and time bottleneck in practice and the main hurdle for assembling large genomes. This problem is compounded because state-of-the-art assemblers do not build the de Bruijn graph for a single order (value of K) but for multiple values of K: they builddde Bruijn graphs, each with a specific order, i.e., GK1, GK2, GKd. Al-though, this paradigm increases the quality of the assembly produce but it greatly increases runtime, because of the need to construct graphs instead of one. In this paper, we show how to augment a succinct de Bruijn graph representation by Bowe et al. (Proc. WABI, 2012) to support new operations that let us change order on the fly, effectively representing all de Bruijn graphs of order up to some maximum Kin a single data structure. Our experiments show our variable-order de Bruijn graph only modestly increases space usage, construction time, and navigation time compared to a single order graph.