Producing Genomic Sequences after Genome Scaffolding with Ambiguous Paths: Complexity, Approximation and Lower Bounds - LIRMM - Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier Access content directly
Journal Articles Algorithmica Year : 2021

Producing Genomic Sequences after Genome Scaffolding with Ambiguous Paths: Complexity, Approximation and Lower Bounds

Abstract

Scaffolding is the final step in assembling Next Generation Sequencing data, in which pre-assembled contiguous regions ("contigs") are oriented and ordered using information that links them (for example, mapping of paired-end reads). As the genome of some species is highly repetitive, we allow placing some contigs multiple times, thereby generalizing established computational models for this problem. We study the subsequent problems induced by the translation of solutions of the model back to actual sequences, proposing models and analyzing the complexity of the resulting computational problems. We find both polynomialtime and N P-hard special cases like planarity or bounded degree. Finally, we propose two polynomial-time approximation algorithms according to cut/weight score.
Fichier principal
Vignette du fichier
producing_genome.pdf (672.62 Ko) Télécharger le fichier
Origin : Files produced by the author(s)

Dates and versions

lirmm-03218029 , version 1 (05-05-2021)
lirmm-03218029 , version 2 (03-06-2021)

Identifiers

Cite

Tom Davot, Annie Chateau, Rodolphe Giroudeau, Mathias Weller, Dorine Tabary. Producing Genomic Sequences after Genome Scaffolding with Ambiguous Paths: Complexity, Approximation and Lower Bounds. Algorithmica, 2021, 83, pp.2063-2095. ⟨10.1007/s00453-021-00819-6⟩. ⟨lirmm-03218029v2⟩
148 View
156 Download

Altmetric

Share

Gmail Facebook X LinkedIn More