Microbial Genomics Training in Lyon

Microbial genomics and metagenomics combine sequencing technologies and computational analysis to profile microbial communities, characterize genomes, and detect functional traits such as antimicrobial resistance.

This instructor-led, live training (online or onsite) is aimed at beginner-level to intermediate-level researchers and bioinformaticians who wish to perform hands-on analysis of microbial genomics and metagenomic sequencing data.

By the end of this training, participants will be able to:

• Describe common sequencing workflows and key file formats used in microbial genomics.
• Perform quality control and preprocessing of raw NGS reads.
• Carry out taxonomic profiling using marker-based and k-mer approaches.
• Assemble and annotate microbial genomes and plasmids.
• Detect SNPs, build phylogenies, and interpret population structure.
• Predict antimicrobial resistance genes and summarize functional profiles.
• Use reproducible workflows with Conda, Docker, and notebook-based reports.

Format of the Course also allows for the evaluation of participants.

• Lectures introducing concepts and tools (20%).
• Hands-on practical sessions using example datasets (60%).
• Open discussions and guided analysis so participants can apply methods to their data (20%).

Course Customization Options

• To request a customized workshop focusing on clinical, environmental, or industrial metagenomics, please contact us to arrange.