A Graph Constraints Formulation for Contigs Scaffolding

Eric Bourreau 1 Annie Chateau 2 Clément Dallard 1 Rodolphe Giroudeau 1
1 MAORE - Méthodes Algorithmes pour l'Ordonnancement et les Réseaux
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
2 MAB - Méthodes et Algorithmes pour la Bioinformatique
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
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.
Keywords : scaffold
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Conference papers
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Submitted on : Monday, September 5, 2016 - 6:54:22 PM
Last modification on : Friday, March 29, 2019 - 6:29:07 PM
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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⟩

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