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Journal Articles Algorithms for Molecular Biology Year : 2022

On a greedy approach for genome scaffolding


Background Scaffolding is a bioinformatics problem aimed at completing the contig assembly process by determining the relative position and orientation of these contigs. It can be seen as a paths and cycles cover problem of a particular graph called the “scaffold graph”. Results We provide some NP-hardness and inapproximability results on this problem. We also adapt a greedy approximation algorithm on complete graphs so that it works on a special class aiming to be close to real instances. The described algorithm is the first polynomial-time approximation algorithm designed for this problem on non-complete graphs. Conclusion Tests on a set of simulated instances show that our algorithm provides better results than the version on complete graphs.
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lirmm-03835013 , version 1 (31-10-2022)



Tom Davot, Annie Chateau, Rohan Fossé, Rodolphe Giroudeau, Mathias Weller. On a greedy approach for genome scaffolding. Algorithms for Molecular Biology, 2022, 17 (1), pp.16-46. ⟨10.1186/s13015-022-00223-x⟩. ⟨lirmm-03835013⟩
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