Genome reassembly with high-throughput sequencing data

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