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.
Eric Bourreau, Annie Chateau, Clément Dallard, Rodolphe Giroudeau. A Graph Constraints Formulation for Contigs Scaffolding. WCB: Workshop on Constraint-Based Methods for Bioinformatics, Sep 2016, Toulouse, France. pp.136-149. ⟨lirmm-01360463⟩
