An Integer Linear Programming Approach for Scaffolding Based on Exemplar Breakpoint Distance.

Reference-based scaffolding is an important process used in genomic sequencing to order and orient the contigs in a draft genome based on a reference genome. In this study, we utilize the concept of genome rearrangement to formulate this process as an exemplar breakpoint distance (EBD)-based scaffolding problem, whose aim is to scaffold the contigs of two given draft genomes, both containing duplicate genes (or sequence markers) and acting with each other as a reference, such that the EBD between the scaffolded genomes is minimized. The EBD-based scaffolding problem is difficult to solve because it is non-deterministic polynomial-time (NP)-hard.