Optimal Scaffolding for Chloroplasts' Inverted Repeats
Year: 2022
Type: conference-paper
Abstract: 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.
Source: HAL
Language: French
Subfield: Genetics
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W4285533641