This training session is organized by the Genotoul bioinfo platform. This course is dedicated to the analysis of prokaryotic shotgun metagenomic data from Illumina and Pacbio HiFi sequencing technology.

After an overview of metagenomics and the biases and limitations of analyses, we will look at the main steps involved in analysing metagenomic data and launch independent tools on the genobioinfo cluster.
Learners will then test a workflow to automate processing on a test dataset (metagWGS ).
On the third day, learners will choose which analysis strategy to start with according to their experimental design and launch the first stage of metagWGS on their own data.
By the end of the course, trainees will be familiar with the scope, advantages and limitations of shotgun sequencing data analysis and will have started the analysis on their own data.

calendar


This training is focused on practice. It consists of several modules with a large variety of exercises:

First Day
Start at 09:00 am
Tour de table
Introduction to metagenomics, Illumina and Pacbio data, analysis stages, analysis limits, etc.
Presentation of some key tools for each stage
Practical work on the main stages launched independently
End at 17:00 pm
Second Day
Start at 09:00 am
Introduction to the advantages and disadvantages of workflows and containers
Launch of the data cleansing stage
Launch of the rest of the workflow and analysis of the multiQC report
End at 17:00 pm
Third Day – BYOD
Start at 09:00 am
Define the analysis strategy and launch the start of the analysis of your own data.
End at 17:00 pm maximum