Global optimization approach for circular and chloroplast genome assembly

Francois, S.; Andonov, R.; Lavenier, D.; Djidjev, H.

doi:10.1101/231324

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bioRxiv · 10.1101/231324

Global optimization approach for circular and chloroplast genome assembly

Francois, S.·Andonov, R.·Lavenier, D.·Djidjev, H.

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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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Francois, S., Andonov, R., Lavenier, D., Djidjev, H.. 2017-12-11. Global optimization approach for circular and chloroplast genome assembly. https://doi.org/10.1101/231324

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