Metagenomics analysis is the study of DNA extracted directly from environmental samples (e.g., soil, water, or on individuals like gut, nose, saliva).
It allows the identification of communities of microbes (bacteria, archea, viruses) living on or inside locations/individuals. In particular their diversity and relationships, as well as their functions and interactions.
It is based on high throughput sequencing of either Whole Genome Shotgun (WGS) or targeted via some specific genes (e.g., 16S, 18S, ITS, etc...). The sequences are then analyzed using bioinformatics methods to extract OTU or ASV count tables (e.g., BIOM format) or Metagenome Assembled Genomes (MAGs).
The downstream analysis of these datasets is still a very active field in research. In this course we will review the various methods currently used starting from the generation of sequences to the final downstream analysis.
- Enseignant·e: Laurent Falquet
- Enseignant·e non éditeur: Patrick Favre