UC San Diego

Optical mapping is a DNA physical mapping technique that can measure large-scale structural variation in genomes and enables more accurate completion of genome assemblies. Particularly, we focus on the case where optical mapping is used to complete genome assembly on pre-identified segments such as may be found in a breakpoint graph. In this work we study methods for aligning optical map contigs with reference genome segments. This work introduces a novel method for optical map alignment that outperforms existing methods for aligning breakpoint graph reference segments to assembled optical map contigs. Also discussed are some additional modifications that can be made to the method.