Séminaire du Pôle SDD – Invité : Dr. Christopher Quince (University of Warwick, UK)
25 avril @ 11 h 00 min - 12 h 30 min
Le pôle SDD recevra Dr Christopher Quince (University of Warwick, UK) au LS2N
jeudi 25 avril à 11h
dans l’amphi du bâtiment 34, sur le site FST (arrêt tram Michelet Science).
Ce dernier donnera un séminaire intitulé : “ Resolving de novo strain variation from metagenomes for high resolution analysis of microbiomes « .
The importance of strain level variation in the human microbiome is well established. Short read metagenomics has the resolution to resolve strains but most current approaches require reference genomes. Methods for de novo resolving strains are still an area of active development. Strains cannot be simply assembled from metagenomes due to the complexity of the assembly graph when multiple closely related genomes are present. This results in fragmented assemblies of potentially millions of contigs. It is possible to cluster or bin contigs into metagenome assembled genomes (MAGs) using composition and co-occurrence across multiple samples. I will introduce our binning algorithm CONCOCT and illustrate its application to both environmental and human-associated microbial communities. However, the MAGs that result from metagenome binning are still composites of multiple strains. I will also demonstrate how co-occurrence across samples can also be used to resolve sub populations within MAGs, using our DESMAN (De novo extraction of strains from metagenomes) pipeline. This leads to a higher resolution picture of microbial community changes.
Un café d’accueil sera offert à partir de 10h30 dans le hall du bâtiment 34.