Environmental Metagenomics


11-15 November 2024

To foster international participation, this course will be held online



Metagenomics is a widely used tool for the analysis of microbial communities as it gives access to the genomes of uncultured microorganisms. Particularly in complex ecosystems (e.g. soil), currently uncultured taxa typically comprise a large fraction of the microbial communities. Metagenomics has many benefits compared to amplicon sequencing, as it gives information not only on the taxonomic diversity but also on the functional composition of microbial communities.

 Recent bioinformatic developments now allow the recovery of metagenome-assembled genomes (MAGs) at an incredible depth.  


During this one-week course you will learn state-of-the-art bioinformatic approaches to analyse metagenomic data. We will cover both read- and assembly-based methods, focusing on the strength of each of these methods depending on the research question. We will use data from both short- (e.g. Illumina) and long-read (e.g. Nanopore) sequencing platforms, as this combination dramatically improves MAG assemblying and binning compared to short-read-only methods.


We assume some basic awareness of analysis  of UNIX and molecular biology.



By completing this course, you will:
- Understand the basics of metagenomic sequencing and bioinformatic approaches for the analysis of metagenomic data
- Be able to plan and execute a metagenomic sequencing project
- Have an up-to-date knowledge on the bioinformatic tools and best practices for the analysis of metagenomes
- Be able to choose the right tools and approaches to answer your specific research question
- Have confidence to learn new methods needed to answer your research question


Monday - 9 am -1 pm Berlin time  

Course outline and practical info
Introduction to metagenomics
Setting up the cloud computing
Getting the raw data

Tuesday - 9 am -1 pm Berlin time  

QC and trimming
Read-based taxonomic profiling

Wednesday - 9 am -1 pm Berlin time  

Genome-resolved metagenomics

Automatic binning with SemiBin2

Thursday - 9 am -1 pm Berlin time  


Quality control of metagenome-assembled genomes (MAGs) with checkM2/GUNC

Annotating your MAGs taxonomically/functionally, using GTDB-Tk, pyrodigal, and eggnog-mapper
Exploration of results/discussion

Friday - 9 am - 1 pm Berlin time  

Targeted functional analysis of MAGs, example using antibiotic resistance genes
Open questions and discussion



COst overview

Package 1


530 €


Cancellation Policy:




> 30  days before the start date = 30% cancellation fee


< 30 days before the start date= No Refund.




Physalia-courses cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.