On a greedy approach for genome scaffolding - LIRMM - Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier Access content directly
Journal Articles Algorithms for Molecular Biology Year : 2022

On a greedy approach for genome scaffolding

Abstract

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.
Fichier principal
Vignette du fichier
on_a_greedy_approach_for_genome_scaffolding.pdf (827.65 Ko) Télécharger le fichier
Origin Files produced by the author(s)

Dates and versions

lirmm-03835013 , version 1 (31-10-2022)

Identifiers

Cite

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⟩
55 View
33 Download

Altmetric

Share

Gmail Mastodon Facebook X LinkedIn More