Optimal Scaffolding for Chloroplasts' Inverted Repeats - Inria - Institut national de recherche en sciences et technologies du numérique Access content directly
Conference Papers Year :

Optimal Scaffolding for Chloroplasts' Inverted Repeats

Scaffolding Optimal pour les Régions Répétées Inverses-Complémentaires de Génome de Chloroplastes


Scaffolding step in the genome assembly aims to determine the order and the orientation of a huge number of previously assembled genomic fractions (contigs/scaffolds). Here we introduce a particular case of this problem and denote it by Nested Inverted Fragments Scaffolding (NIFS). We formulate it as an optimisation problem in a particular kind of directed graph that we call Multiplied Doubled Contigs Graph (MDCG). Furthermore, we prove that the NIFS problem is NP-Hard. We also discuss how the chloroplast data have been generated by filtering the reads sequenced both from plants and chloroplasts. Moreover, we propose a graph structure to visualise the solution and to highlight the particularity of chloroplast's regions structure.
Fichier principal
Vignette du fichier
JOBIM_2022_KhloraaScaf.pdf (499.75 Ko) Télécharger le fichier
Origin : Files produced by the author(s)

Dates and versions

hal-03625229 , version 1 (30-03-2022)


  • HAL Id : hal-03625229 , version 1


Victor Epain, Rumen Andonov, Dominique Lavenier. Optimal Scaffolding for Chloroplasts' Inverted Repeats. JOBIM2022, Jul 2022, Rennes, France. ⟨hal-03625229⟩
50 View
25 Download


Gmail Facebook Twitter LinkedIn More