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Joint NFDI4Microbiota/ELIXIR-DE Metagenomics training course (Oct 6th-7th 2022)

The microbiome is the ecological community of commensal, symbiotic and pathogenic microorganisms found in and on all multicellular organisms from plants to animals. The microbiome has been found to be crucial for immunologic, hormonal and metabolic homeostasis of its host. In this workshop, we aim to not only introduce you to the all the necessary basic methods to analyse a microbiome experiment, like processing your raw data, statistical testing and quality control. We also want to practice these computational techniques in interactive hands-on sessions. On the second day, we want to introduce you to visual applications for research analysis. First, we will introdcue Qiita, a microbial study management platform used to manage and compute studies with microbiome data. This framework establishes an easily accessible way for non-computational scientists to analyse their own data with the option of using pre-defined workflows or building their own. The different options on how to utilize the previously learned basics in Qiita will be explored in further hands-on sessions. Afterwards, we're going to focus on WGS metagenomics data, where several recent approaches tackling the problem of taxonomic assignment will be presented. Finally, the MGX framework will be introduced, a modern graphical application that allows researchers to perform taxonomic and functional classification without the need for any programming expertise or large-scale compute resources.




  • Thursday, October 6th

10:00-11:00 Introduction

11:00-12:30 From raw data to feature tables

12:30-13:30 Lunch break

13:30-14:30 Statistical testing

14:30-15:00 Coffee break

15:00-16:30 Sequence quality control (incl. Hands-on)


  • Friday, October 7th

10:00-10:30 QIIME2 and Qiita

10:30-11:30 Qiita Hands-On

11:30-11:45 Coffee break

11:45-12:30 Qiita Hands-On (cont'd.)

12:30-13:30 Lunch break

13:30-14:30 Metagenomics

14:30-15:00 Coffee break

15:00-16:00 Metagenome analysis with MGX

16:00-16:15 Closing remarks


Registration & Venue

This workshop is an in-person event and participation is free of charge; the workshop will take place at

the old chemistry building of the Justus Liebig University, Heinrich-Buff-Ring 58, 35392 Giessen, in rooms

0024a (workshop) and 0001 (coffee breaks and lunch). Once you enter the building, the way to the workshop

will be sign-posted.


The number of participants is limited to 20. Registration is closed as we're already booked out.



We can recommend that you make your reservation at one of the following venues:


Local organizers


Prof. Dr. Stefan Janssen (NFDI4Microbiota)

Anna Rehm (NFDI4Microbiota)

Dr. Sebastian Jaenicke (ELIXIR-DE)


Contact in case you have any questions.