Global optimization approach for circular and chloroplast genome assembly

Sébastien Francois 1 Rumen Andonov 1 Dominique Lavenier 1 Hristo Djidjev 2
1 GenScale - Scalable, Optimized and Parallel Algorithms for Genomics
Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
Abstract : We describe a global optimization approach for genome assembly where the steps of scaffolding, gap-filling, and scaffold extension are simultaneously solved in the framework of a common objective function. The approach is based on integer programming model for solving genome scaffolding as a problem of finding a long simple path in a specific graph that satisfies additional constraints encoding the insert-size information. The optimal solution of this problem allows one to obtain new kind of contigs that we call distance-based contig. We test the algorithm on a benchmark of chloroplasts and compare the quality of the results with recent scaffolders.
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Sébastien Francois, Rumen Andonov, Dominique Lavenier, Hristo Djidjev. Global optimization approach for circular and chloroplast genome assembly. BICoB 2018 - 10th International Conference on Bioinformatics and Computational Biology, Mar 2018, Las Vegas, United States. pp.1-11, ⟨10.1101/231324⟩. ⟨hal-01666830⟩

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