Global optimization for scaffolding and completing genome assemblies

DOI10.1016/j.endm.2018.01.020zbMath1388.92027OpenAlexW2604269101MaRDI QIDQ1742221

Dominique Lavenier, Sebastien François, Rumen Andonov, Hristo N. Djidjev

Publication date: 11 April 2018

Full work available at URL: https://hal.inria.fr/hal-01499859/file/RR-9050%20%281%29.pdf

Mathematics Subject Classification ID

Mixed integer programming (90C11) Linear programming (90C05) Protein sequences, DNA sequences (92D20)

Uses Software

• Gurobi
• GRASS
• QUAST
• BESST
• ScaffMatch
• ART

Cites Work

• Exact methods for solving the elementary shortest and longest path problems
• The greedy path-merging algorithm for contig scaffolding
• An Eulerian path approach to DNA fragment assembly

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