A Graph Constraints Formulation for Contigs Scaffolding

Abstract : This paper presents a constraint-based approach for genome scaffolding, which is one important step in genome whole sequence pro- duction. We model it as an optimization problem on a graph built from a paired-end reads mapping on contigs. We describe our constraint model using a graph variable representation with classical graph constraints. We tested our approach together with several search strategies, on a benchmark of various genomes.