Recent studies in genomics have highlighted the significance of structural variation in deter-
mining individual variation. Current methods, however, are predominantly focused on either
assembling whole genomes from scratch, or identifying the relatively small changes between
a genome and a reference sequence. While significant progress has been made in recent years
on both de novo assembly and resequencing (read mapping) methods, few attempts have
been made to bridge the gap between them.
In this paper, we present a computational method for incorporating a reference sequence
into an assembly algorithm. We propose a novel graph construction that builds upon the
well-known de Bruijn graph to incorporate the reference, and describe a simple algorithm,
based on iterative message passing, which uses this information to significantly improve
assembly results. We validate our method by applying it to a series of 5Mb simulation
genomes derived from both mammalian and bacterial references. The results of applying
our method to this simulation data are presented along with a discussion of the benefits and
drawbacks of this technique.