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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Communication dans un congrès
BICoB 2018 10th International Conference on Bioinformatics and Computational Biology, Mar 2018, Las Vegas, United States
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Dernière modification le : jeudi 11 janvier 2018 - 06:28:15

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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. 〈hal-01666830〉

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