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Conference Papers Year : 2016

Global Optimization Methods for Genome Scaffolding


We develop a method for solving genome scaffolding as a problem of finding a long simple path in a graph defined by the contigs that satisfies additional constraints encoding the insert-size information. Then we solve the resulting mixed integer linear program to optimality using the Gurobi solver. We test our algorithm on several chloroplast genomes and show that it is fast and outperforms other widely-used assembly algorithms by the accuracy of the results.
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hal-01385665 , version 1 (21-10-2016)


  • HAL Id : hal-01385665 , version 1


Sebastien François, Rumen Andonov, Hristo Djidjev, Dominique Lavenier. Global Optimization Methods for Genome Scaffolding. 12th International Workshop on Constraint-Based Methods for Bioinformatics , Sep 2016, Toulouse, France. ⟨hal-01385665⟩
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