We describe a global optimization approach for
genome assembly where the steps of scaolding, gap-
lling, and scaold extension are simultaneously solved
in the framework of a common objective function.
The approach is based on integer programming
model for solving genome scaolding as a problem of
nding a long simple path in a specic graph that
satises additional constraints encoding the insert-size
information. The optimal solution of this problem
allows one to obtain new kind of contigs that we call
distance-based contig. We test the algorithm on a
benchmark of chloroplasts and compare the quality of
the results with recent scaolders.