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Conference Papers Year : 2016

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.
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Dates and versions

lirmm-01360463 , version 1 (05-09-2016)

Identifiers

  • HAL Id : lirmm-01360463 , version 1

Cite

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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