BACKGROUND
The increasing usage of exciting metabarcoding approaches poses a problem for many students and researchers: the steep learning curve of programming languages and command line interfaces can be frustrating and a lot of time is wasted searching for typing errors, which cannot be invested in actual research.
Galaxy is a free open-source platform, which allows you to analyze data, automatize workflows and gives you time to work on actual problems.
WORKSHOP GOAL
In this 2-days hands-on workshop, participants will learn how to analyse metabarcoding data with Galaxy. You will learn about different tools, get insight into the galaxy project and learn how to generate visualizations of your data only with a few clicks.
The course it suitable for participants with basic knowledge about metabarcoding in their field of science. No prior knowledge about sequence data analyses or command line interfaces is needed.
We will use an example eDNA dataset in this course to practice the analysis workflow. Everybody who wants to participate, but does not have prior knowledge about metabarcoding is welcomed to participate in part 1 of this lecture series.
This course is number 2 out of two courses about metabarcoding, which can be completed individually or as a whole.
Part 1: Overview & Data Management for Metabarcoding (online lecture)
Part 2: Analysis and Visualization with Galaxy (this workshop; 2 days, on campus)
WORKSHOP CONTENT
Day 1: First Steps in Galaxy
- Analysing sequence data with Galaxy
- ASVs vs. OTUs
- QIIME2
- Overview of different approaches and analysis tools
- Different important algorithms
Day 2: Staticial Testing and Visualization
- Statistical tests
- Visualizations with Galaxy and QIIME2
TARGET AUDIENCE & PRIOR KNOWLEDGE
Researchers and (PhD) students who want to learn the basics how to analyse sequence data from metabarcoding approaches and those who want to learn to analyse their data with Galaxy. If you have not visited
Part 1: Overview & Data Management for Metabarcoding of this lecture series, please make sure to know about basic concepts about metabarcoding and data management.
No programming knowledge is needed!
TECHNICAL REQUIREMENTS
Bring your own laptop.
Account at usegalaxy.eu (important: .eu, as we will use the European Galaxy server).
Connection to the Wifi (e.g. via eduroam -> https://www.uni-bremen.de/en/zfn/wifi/overview-wifi) for accessing public datasets and web-based resources.
ABOUT THE TRAINER
Sarah Büker works as Data Scientist at the Data Science Center (University of Bremen). She holds a Bachelor’s degree in Biological Sciences of the University of Osnabrück and a Master’s degree in Marine Environmental Sciences of the University of Oldenburg. In her studies she specialized on ecology and environmental DNA approaches.