Educators:
Sebastian Jaenicke (BiGi), Prof. Dr. Stefan Janssen (NFDI4Microbiota), Anna Rehm (NFDI4Microbiota)
Date:
06.10.2022 – 07.10.2022
Location:
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.
Contents:
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.
Agenda
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)
16:30- Social event
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
Learning goals:
- Quality control and quality assurance
- Taxonomic classification
- Functional assignment
Prerequisites:
- Basic knowledge in microbiology and NGS-based analysis
- Experience with a Linux command line recommended but not required
Keywords:
Microbiome, MGX
Tools:
MGX
Contact & Registration:
The number of participants is limited to 20. Please register in advance.