Environmental Metagenomics


17-21 April 2023

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 strenght 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 it improves dramatically MAG assembling 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 to the analyis 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 -4 pm Berlin time  

    Introduction to metagenomics
    Working with the command line
    QC and trimming

Tuesday - 9 am -4 pm Berlin time  

    Read-based analyses
        Taxonomic annotation of metagenomes
        Functional annotation of metagenomes

Wednesday - 9 am -4 pm Berlin time  

    Metagenome assembly
    Assembly QC

Thursday - 9 am -4 pm Berlin time  

    Genome-resolved metagenomics in anvi'o

Friday - 9 am -4 pm Berlin time  

    Annotation of metagenome-assembled genomes (MAGs) and downstream analyses




Dr. Antti Karkman





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.