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.

CSAR: a contig scaffolding tool using algebraic rearrangements.

Summary: Advances in next generation sequencing have generated massive amounts of short reads. However, assembling genome sequences from short reads still remains a challenging task. Due to errors in reads and large repeats in the genome, many of current assembly tools usually produce just collections of contigs whose relative positions and orientations along the genome being sequenced are still unknown.