Global Optimization for Scafolding and Completing Genome Assemblies
Résumé
We develop a method for solving genome scafolding 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 outperforms other widely-used assembly solvers by the accuracy of the results.
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