The Syntenic Path Assembly is an option in SynMap to do a reference genome assembly of contigs using synteny to determine the order and orientation of the contigs.
SynMap analysis of a WGS assembly of a strain of E. coli K12 (y-axis) to a reference assembly (x-axis) using SynMap's Syntenic Path Assembly to order contigs. Results may be regenerated at:
http://genomevolution.org/r/2k71