Clément Agret defended his thesis on 13 October 2020. Carried out in the framework of the GenomeHarvest flagship project, and funded by Agropolis Fondation, his topic was on "Development of indexing compressed structures for analyzing collection of similar genomes: application to rice genomes."
Clément has been supervised by Manuel Ruiz, Alban Mancheron and Annie Chateau and hosted at Montpellier, SupAgro , in the framework of Biodiversity, Agriculture, Food, Environment, Land, Water , in partnership with AGAP - Amélioration Génétique et Adaptation des Plantes (laboratory) and Data Integration (DI) (research team) since 01-09-2016 .
The subject of my thesis concerns the study of index structures and compression methods to find a solution to the problem of indexing a collection of similar genomes. The ultimate goal is to apply these methods to the indexation of rice genomes and to facilitate the analysis of the impact of their structural variations on recombination rates, allele frequencies, GWAS studies, Other activities of GenomeHarvest. The indexation of complete genomes is an important stage in the exploration and understanding of data from living organisms. An index should provide a quick answer to the following questions: - How many times a given pattern appear in the genome? - Which are the positions of a given pattern? - What is the pattern length at the i position in the genome?