From Data to Discovery: Metagenomics, RNA-Seq - NGS Bioinformatics with Galaxy
In-person course
This course introduces scientists to the data analysis platform Galaxy. The course is a beginner course; no programming skills are required.
Welcome to the Comprehensive Galaxy Workshop: From Introduction to Advanced Applications
Embark on a deep dive into the world of Galaxy, the leading platform for data-intensive biomedical research. This workshop is designed for researchers, students, and data analysts who wish to harness the full potential of Galaxy in transcriptomic, single-cell and metagenomics studies. Whether you’re a beginner seeking to understand the basics or an intermediate user looking to refine your skills in specific applications, this workshop offers valuable insights and hands-on experiences.
This comprehensive workshop will increase your proficiency in using Galaxy and enhance your ability to conduct sophisticated analyses in various fields of biological research. Connect with experts and peers, gain practical skills, and take your research capabilities to the next level.
Topics
- Galaxy Introduction and Quality Control
- RNA-seq Analysis
- Single-Cell sequencing
- Microbiome Analysis
Learning Objectives
- To get introduced to Galaxy as a data analysis platform and the GTN training material
- To learn how to use tools and databases in Galaxy
- To be able to run different tools and workflows
Schedule
Please see the Program tab.
Registration
The number of places in this workshop is limited. The course takes place only in person (not online, not hybrid). There are no fees for the workshop but you need to care for your accommodation, travel costs and catering yourself.
Who is this course for?
Scientists with no or little Galaxy experience who want to analyse sequencing data.Event Location
Geocoding via Nominatim, Map data from OpenStreetMap
Organisers & Instructors
This event is brought to you by:
| Organiser(s) |
Daniela Schneider 
Teresa Müller
|
| Instructor(s) |
Pavankumar Videm
Teresa Müller
Diana Chiang Jurado
Engy Nasr
Paul Zierep
Mina Hojat Ansari
|
Before you start
Before starting the course, make sure to follow the setup instructions
Monday: Introduction and Quality Control
We will do at least one coffee break in the morning, one in the afternoon, and a one-hour lunch break around noon.
| Time | Lesson | Slides | Hands-on | Recordings |
|---|---|---|---|---|
09:15 |
Welcome |
|||
|
From peaks to genes
|
||||
|
Quality Control
|
||||
16:00 |
End |
|||
Tuesday: RNA Sequencing
We will do at least one coffee break in the morning, one in the afternoon, and a one-hour lunch break around noon.
| Time | Lesson | Slides | Hands-on | Recordings |
|---|---|---|---|---|
09:15-17:00 |
Reference-based RNA-Seq data analysis |
Wednesday: Single-Cell Sequencing
We will do at least one coffee break in the morning, one in the afternoon, and a one-hour lunch break around noon.
| Time | Lesson | Slides | Hands-on | Recordings |
|---|---|---|---|---|
09:15-17:00 |
Clustering 3K PBMCs with Scanpy |
Thursday: Metagenomics
We will do at least one coffee break in the morning, one in the afternoon, and a one-hour lunch break around noon.
| Time | Lesson | Slides | Hands-on | Recordings |
|---|---|---|---|---|
09:15 |
Start |
|||
| Taxonomic Profiling and Visualization of Metagenomic Data | ||||
| Calculating α and β diversity from microbiome taxonomic data | ||||
16:00 |
End |
|||
Friday: Metagenomics
We will do at least one coffee break in the morning, one in the afternoon, and a one-hour lunch break around noon.
| Time | Lesson | Slides | Hands-on | Recordings |
|---|---|---|---|---|
09:15-16:00 |
Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition |
Get set up for the course!
Follow the steps below to get set up with everything you need to participate in the course!
Create a Galaxy Account
Create an account on one of the following Galaxy servers:
You will get an email with activation link. It may end up in your junk folder.
Note: If you already have a Galaxy account you can skip this step and just log in to your existing account.
Join Galaxy Training Group (TIaaS)
Join TIaaS by clicking on the link below matching your Galaxy server:
- Galaxy EU is not using TIaaS
This will give your analysis jobs priority on Galaxy for the duration of the event. Make sure you are logged in before clicking the link. You should see a green message box if all went well.
Instructor Zone
Check out our checklists for
- Organising a Workshop to check that you haven't forgotten any important step.
- Running a Workshop, helpful reminders closer to your event.
Request TIaaS
Training Infrastructure as a Service (TIaaS) is a service that allows you to request space for your course on a server, it helps ensure courses run smoothly by separating your trainee's jobs into a separate queue. Learn more about TIaaS in our tutorial.
The following links will open a (mostly) pre-filled out TIaaS form,
Once you receive a URL from the admins, please set it as a tiaas_link in your event metadata.
Add your event to the Galaxy Hub Event Horizon
To also list your event on the Galaxy Event Horizon, copy the text below, and add your event to the Galaxy Hub GitHub Repo. Create a folder for your event here, and add an index.md file with the following contents:
---
title: "From Data to Discovery: Metagenomics, RNA-Seq - NGS Bioinformatics with Galaxy"
date: '2025-06-30'
days: 5
tease: This course introduces scientists to the data analysis platform Galaxy. The course is a beginner course; no programming skills are required.
#continent: EU
location: "University of Freiburg,Freiburg"
external_url: "https://training.galaxyproject.org/training-material/events/2025-06-30-hts-workshop-freiburg.html"
gtn: true
contact: "schneidd@informatik.uni-freiburg.de"
subsites: [all]
---
Promote the Event
Tootable/Tweetable version:
From Data to Discovery: Metagenomics, RNA-Seq - NGS Bioinformatics with Galaxy! 📢
This course introduces scientists to the data analysis platform Galaxy. The course is a beginner course; no programming skills are required.
📅 June 30 – July 4, 2025
➡️ https://gxy.io/GTN:E00015
📝 Registration is open until 2025-05-11! https://forms.gle/AQ7n7zi1rUd995Me9
Slack-compatible version:
From Data to Discovery: Metagenomics, RNA-Seq - NGS Bioinformatics with Galaxy! 📢
This course introduces scientists to the data analysis platform Galaxy. The course is a beginner course; no programming skills are required.
:calendar: June 30 – July 4, 2025
:arrow_right: https://gxy.io/GTN:E00015
:pencil: Registration is open until 2025-05-11! https://forms.gle/AQ7n7zi1rUd995Me9
Version with schedule:
From Data to Discovery: Metagenomics, RNA-Seq - NGS Bioinformatics with Galaxy! 📢
This course introduces scientists to the data analysis platform Galaxy. The course is a beginner course; no programming skills are required.
**Agenda**:
- Monday: Introduction and Quality Control
- Tuesday: RNA Sequencing
- Wednesday: Single-Cell Sequencing
- Thursday: Metagenomics
- Friday: Metagenomics
📅 June 30 – July 4, 2025
➡️ https://gxy.io/GTN:E00015
📝 Registration is open until 2025-05-11! https://forms.gle/AQ7n7zi1rUd995Me9
Register Now!
Deadline: 11 May 2025
Event details
| event-date | June 30 – July 4, 2025 |
| event-location | University of Freiburg, Werthmannstrasse 4, Freiburg, Germany, 79104 |
| event-cost | free |
| schneidd@informatik.uni-freiburg.de |
Add this event to your calendar Google Outlook Office 365
Organisers
Daniela Schneider
Teresa Müller
Instructors
Pavankumar Videm
Teresa Müller
Diana Chiang Jurado
Engy Nasr
Paul Zierep
Mina Hojat Ansari
In collaboration with
EuroScienceGateway
de.NBI
DataPLANT