Environmental Metagenomics

Dates

13-17 October 2025

To foster international participation, this course will be held online

 

OVERVIEW

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.

Prerequisites

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

 

Outcomes

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

Program

Monday (9 am - 1 pm CET)

  • Course introduction and practical info
  • Introduction to metagenomics
  • Setting up cloud computing (hands-on)
  • Retrieving raw data (hands-on)

Tuesday (9 am - 1 pm CET)

  • Q&A from previous day
  • Quality control and trimming (slides & hands-on)
  • Metagenome assembly (slides & hands-on)
  • Assembly quality control (hands-on)
  • Read-based taxonomic profiling (slides & hands-on)

Wednesday (9 am - 1 pm CET)

  • Q&A from previous day
  • Continued read-based taxonomic profiling (slides & hands-on)
  • Genome-resolved metagenomics using anvi'o (slides & hands-on)

Thursday (9 am - 1 pm CET)

  • Q&A from previous day
  • Continued genome-resolved metagenomics using anvi'o (slides & hands-on)
  • Continued read-based taxonomic profiling (slides & hands-on)

Friday (9 am - 1 pm CET)

  • Continued read-based taxonomic profiling (slides & hands-on)
  • Quality control and taxonomic annotation of MAGs (hands-on)
  • Automatic binning with SemiBin2 (hands-on)
  • Sharing MAG information
  • Targeted functional analysis of MAGs (hands-on)
  • Open Q&A 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.