Overview of the map assembly pipeline. Reference maps are generated in silico from the NCBI Build 35 human genome reference sequence, and used to seed an iterative process of pairwise alignment (which clusters together similar single-molecule maps) and local assembly (which generates a consensus optical map from a cluster of single-molecule maps). After several iterations of alignment and assembly, the consensus maps are aligned back to the reference map and analyzed for places where the consensus map differs significantly from the reference.