Global Optimization for Scaffolding and Completing Genome Assemblies - Inria - Institut national de recherche en sciences et technologies du numérique Access content directly
Journal Articles Electronic Notes in Discrete Mathematics Year : 2018

Global Optimization for Scaffolding and Completing Genome Assemblies

Abstract

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 outperforms other widely-used assembly solvers by the accuracy of the results. ⋆ Preliminary version of this paper has been presented at the Workshop on Constraint-Based Methods for Bioinformatics 2016.
Fichier principal
Vignette du fichier
main.pdf (259.06 Ko) Télécharger le fichier
Origin : Files produced by the author(s)

Dates and versions

hal-03697534 , version 1 (17-06-2022)

Identifiers

  • HAL Id : hal-03697534 , version 1

Cite

Sebastien François, Rumen Andonov, Dominique Lavenier, Hristo Djidjev. Global Optimization for Scaffolding and Completing Genome Assemblies. Electronic Notes in Discrete Mathematics, 2018. ⟨hal-03697534⟩
18 View
25 Download

Share

Gmail Facebook X LinkedIn More