Training courses & workshops

In the context of the 4th NFDI4Microbiota Annual Conference 2025 , from September 30th till October 2nd 2025 in Cologne, we cordially welcome you to join our workshop From Bench to Browser: Microbiome Analysis Without Coding Skills

The following zip archive contains demo data for the workshop. Download via our JLU box and extract with any *.zip compatible progranm: Qiita workshop demo data (~66 MB)

Here you can find the slides as a PDF for the hands-on session: Slides

We are happy to be part of the 3rd Old-Herborn University Summer School 2025 .

You can here download the Jupyter notebook for the hands on session.

The PDF slide-deck from the lecture can be downloaded here.

The microbiome is the ecological community of commensal, symbiotic and pathogenic microorganisms found in and on all multicellular organisms from plants to animals. It 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. Additionally, we want to introduce you to 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. Afterwards, we will explore the microbiome analysis pipeline QIIME2 to delve further into our data sets and to enable you to be able to take your first steps towards your own analysis.

!Construction Site!

Should you arrive via bus (lines 3 or 10 or 13, stop: "Arndtstraße"), please be aware of a construction site that is currently blocking the direct way to our building. You need to follow the pink path (there are some but not all necessary redirections signs). Go downhill, make a right turn, enter the parking lot, cross the lot diagonally and leave through a silver gate. You now are in front of our ugly, tall building, surrounded by a construction fence. Go uphill until you can make a left turn. Go down again until you see the sliding glass door entry of the "north" entry. The next room to your right is our meeting location. See you soon!

Agenda

Tuesday, October 8th

• 11:00-11:30 Introduction
• 11:30-13:00 From raw data to feature tables
• 13:00-14:00 Lunch break
• 14:00-14:30 Sequence quality control
• 14:30-15:00 Coffee break
• 15:00-16:30 Sequence quality control Hands-on

Wednesday, October 9th

• 10:00-10:30 QIIME2 and Qiita
• 10:30-11:30 Qiita Hands-On ( ForQiita_p1.zip part 1 of 2 data package , ForQiita_p2.zip part 2 of 2 data package )
• 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 QIIME2 Hands-On
• 14:30-15:00 Coffee break
• 15:00-15:30 Diversity Calculation
• 15:30-16:00 QIIME2 Hands-On (cont'd.)

Thursday, October 10th

• 10:00-11:30 Buffer for Hands-On, Coffee break in-between ( rep-seq.qza ), ( taxAssignments.qza )
• 11:30-11:45 Coffee break in-between
• 11:45-12:30 Buffer for Hands-On
• 12:30-13:30 Closing remarks and Farewell

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 room 0024a . Once you enter the building, the way to the workshop will be sign-posted.

The maximum amount of participants has been reached and registration is now closed. If you have further questions, please write an e-mail to metagenomics2024@computational.bio .

Accomodation

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

• Parkhotel Sletz
• Cityhotel Giessen

Local organizers

Prof. Dr. Stefan Janssen ( NFDI4Microbiota )

Anna Rehm ( NFDI4Microbiota )