Complete Assembly of Circular and Chloroplast Genomes Based on Global Optimization
This paper focuses on the last two stages of genome assembly, namely scaffolding and gap-filling, and shows that they can be solved as part of a single optimization problem. Our approach is based on modeling genome assembly as a problem of finding a simple path in a specific graph that satisfies as many as possible of the distance constraints encoding the insert-size information. We formulate it as a mixed-integer linear programming problem and apply an optimization solver to find the exact solutions on a benchmark of chloroplasts. We show that the presence of repetitions in the set of unitigs ismore »