A practical workshop for (foodborne) pathogen detection from (direct Nanopore) sequencing data using Galaxy

In-person course

The purpose of this workshop is to gain knowledge on detect (foodborne) pathogens from (direct Nanopore) sequencing data using Galaxy. The workshop will be on October 14th 2024 as a 1-day F2F at FHNW Muttenz, Switzerland, free and practical workshop.

A practical workshop for (foodborne) pathogen detection from (direct Nanopore) sequencing data using Galaxy

Biolytix and the Freiburg Galaxy team teamed up over the last year to develop Galaxy-based workflows for accessible and scalable detection and identification of foodborne pathogens, thanks to an EOSC-Life internal grant for academia-industry collaborations.

To share about the workflows and (foodborne) pathogen detection in general, we organize a 1-day F2F at FHNW Muttenz, Switzerland , free and practical workshop on October 14th, 2025 to learn how to detect (foodborne) pathogens from (direct Nanopore) sequencing data using Galaxy, an open-source platform for FAIR data analysis.

Topics

  • Galaxy Introduction
  • Sequence-analysis
  • Foodborne

Requirements:

  • Knowledge about sequencing techniques
  • Knowledge about pathogens

Learning Outcome

By the end of this workshop, participants will be able to:

  • Name bioinformatics tools and steps required to
    • Preprocess pathogen sequencing data
    • Identify pathogens in sequencing data
    • Track pathogen contamination sources using different sequencing data
  • Repeat steps in Galaxy to preprocess, identify and track pathogens from sequencing data

Schedule

Please see the Program tab.

Registration

The number of places in this workshop is limited.

If you want to register, please contact Diana Hormisch (diana.hormisch@biolytix.ch) or Anna Henger (anna.henger@biolytix.ch)

Getting to FHNW Muttenz

Using Public transport

The FHNW Muttenz Campus is well served by public transport.

  • From Muttenz railway station: A six-minute or so walk via Hofackerstrasse or Grenzacherstrasse and through the campus park.
  • By bus: Bus 46 (from/to Kleinhüngingen) or 47 (from/to Bottmingen) to the “Fachhochschule” stop, then a two-minute walk
  • From the ‘Zum Park’ tram stop in Muttenz: Tram 14 from Basel and Pratteln, then a 10-minute or so walk via Zwinglistrasse and Kriegackerstrasse
  • By train: 5 minutes by train from Basel (S3 direction Olten or S1 direction Frick) and a 5 minute walk from the train station to the campus (see above)

By road

  • Car/motorcycle
    • At the Hagnau junction on the A2 motorway take the A18 towards Delémont then leave by the Muttenz-Nord exit. At the ‘Pantheon’ turn left into Hofackerstrasse.
    • 232 parking spaces are available on Hofackerstrasse (the car park is located on the right-hand side just before the campus). Payment can be made using the FH Card or cash.
    • Parking spaces on the south side of the campus are available for persons with a mobility impairment.
    • More than 50 covered motorcycle parking spaces are available on the west side of the campus (ramp to basement 1)
  • Bicycles: More than 500 covered and uncovered cycle parking spaces are available along Hofackerstrasse and in front of the PTC (Process Technology Centre).

Who is this course for?

Whoever is interested in generating sequencing data to detect pathogens and is interested to learn how to use Galaxy to detect pathogens from sequencing data.

Organisers & Instructors

This event is brought to you by:

Organiser(s) Anna Henger avatar Anna HengerAbdullah Kahraman avatar Abdullah Kahraman
Instructor(s) orcid logoWolfgang Maier avatar Wolfgang Maierorcid logoEngy Nasr avatar Engy NasrSantino Faack avatar Santino Faack

Before you start

Before starting the course, make sure to follow the setup instructions

Preliminary schedule

The workshop will take place on site in Room 02.W.03

Time Lesson Slides Hands-on Recordings

09:30 to 10:00

Welcome

10:00 to 12:00

From peaks to genes

12:00 to 13:00

Lunch

13:00 to 15:30

Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition

15:30 to 16:00

Q&A and Closing

Get set up for the course!

Follow the steps below to get set up with everything you need to participate in the course!

Galaxy logo
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.

cartoon of a person standing in front of a blackboard
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

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, if that server supports TIaaS. Otherwise you might see "page not found".

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: "A practical workshop for (foodborne) pathogen detection from (direct Nanopore) sequencing data using Galaxy"
date: '2025-10-14'
days: 1
tease: The purpose of this workshop is to gain knowledge on detect (foodborne) pathogens from (direct Nanopore) sequencing data using Galaxy. The workshop will be on October 14th 2024 as a 1-day F2F at FHNW Muttenz, Switzerland, free and practical workshop.

#continent: EU
location: "FHNW University of Applied Sciences and Arts Northwestern Switzerland,Muttenz"
external_url: "https://training.galaxyproject.org/training-material/events/2025-10-14-foodborne.html"
gtn: true
contact: "anna.henger@biolytix.ch"
subsites: [all]
---

Promote the Event

Tootable/Tweetable version:


A practical workshop for (foodborne) pathogen detection from (direct Nanopore) sequencing data using Galaxy! 📢

The purpose of this workshop is to gain knowledge on detect (foodborne) pathogens from (direct Nanopore) sequencing data using Galaxy. The workshop will be on October 14th 2024 as a 1-day F2F at FHNW Muttenz, Switzerland, free and practical workshop.


📅 October 14, 2025
➡️ https://training.galaxyproject.org/training-material/events/2025-10-14-foodborne.html

Slack-compatible version:


A practical workshop for (foodborne) pathogen detection from (direct Nanopore) sequencing data using Galaxy! 📢

The purpose of this workshop is to gain knowledge on detect (foodborne) pathogens from (direct Nanopore) sequencing data using Galaxy. The workshop will be on October 14th 2024 as a 1-day F2F at FHNW Muttenz, Switzerland, free and practical workshop.


:calendar: October 14, 2025
:arrow_right: https://training.galaxyproject.org/training-material/events/2025-10-14-foodborne.html

Version with schedule:


A practical workshop for (foodborne) pathogen detection from (direct Nanopore) sequencing data using Galaxy! 📢

The purpose of this workshop is to gain knowledge on detect (foodborne) pathogens from (direct Nanopore) sequencing data using Galaxy. The workshop will be on October 14th 2024 as a 1-day F2F at FHNW Muttenz, Switzerland, free and practical workshop.


**Agenda**:
- Preliminary schedule

📅 October 14, 2025
➡️ https://training.galaxyproject.org/training-material/events/2025-10-14-foodborne.html