Join Us for Optimising Metagenomics Assembled Genomes Building Workflows

Metagenomics Assembled Genomes building workflows are both technically and scientifically challenging, yet they are essential tools for reducing microbial dark matter, as most microbes cannot be cultivated.

As part of the FAIRyMAGs project within the ELIXIR BFSP Programme, we are organizing a 4-day hackathon (October 6-9th) and 1-day for an optional social event (October 10th). We warmly invite the community to join us either in person in Freiburg or online. This event is an opportunity to collaborate, discuss, and improve MAGs workflows together!

FAIRyMAGs is led by Paul Zierep (ELIXIR-DE) and Bérénice Batut (ELIXIR-FR) in collaboration with Giuseppe Defazio (ELIXIR-IT), Bruno Fosso (ELIXIR-IT), Martin Beracochea (EMBL-EBI), Santiago Sanchez (EMBL-EBI), that will be participating the hackathon.

Registration

Registration is free, but the space is limited to 15 attendees, so we recommend to register soon. Please wait for our confirmation before booking your trip. As this is a hybrid event, remote attendance is also possible.

Event Details

• Dates: October 06th–10th, 2025 - This event is right after the European Galaxy Days (EGD), so you have the chance to make it a longer trip to Freiburg and profit from both events.
• Location: Georges-Koehler-Allee 079, D-79110 Freiburg, Germany & Online
• Cost: Free
• Contact: Paul Zierep, Bérénice Batut
• Focus: Enhancing FAIR MAGs building Workflows, Developing user-friendly training materials, Advancing workflow evaluation methods, Building intelligent computational resource estimation tools

Objectives

The objectives of this 4-day scientific and technical hackathon are to optimize Metagenomics Assembled Genomes building by:

• 🚀 Enhancing FAIR MAGs building Workflows

  • Optimizing assembly strategies: Individual assembly vs. co-assembly vs. grouped-assembly, Automating decision-making for assembly selection
  • Bin refinement improvements: Where do we go beyond MetaWrap? Should we integrate more binning tools for better results?
• 📚 Developing user-friendly training materials

• 📊 Advancing workflow evaluation methods (using CAMI infrastructure & real data)

  • Have metagenomic WGS samples? Want to create MAGs? This is your chance!

• ⚙️ Building intelligent computational resource estimation tools

  Whether you're using Nextflow, Snakemake, or Galaxy, resource allocation is key. Over-provisioning wastes resources; under-provisioning leads to failed jobs. Let’s design workflow-agnostic tools that optimize resource usage, reducing computational waste and environmental impact!

Venue

Seminar room in Freiburg Galaxy team building:

Georges-Köhler-Allee 79 79110 Freiburg Germany

Getting to Freiburg

Freiburg can be easily reached by train with the ICE from the North (via Frankfurt and Karlsruhe) and the South (via Basel) Deutsche Bahn.

How to reach Freiburg from Basel/Mulhouse/Freiburg airport (EuroAirport)?

• Option 1: Use the French/German exit and take the airport shuttle bus to Freiburg main station (Hauptbahnhof).
• Option 2: Use the Swiss exit and take the local bus (#50) to the train station in Basel and from there take a train to Freiburg.

How to reach the venue from Freiburg Hauptbahnhof?

• Option 1: Local train; Take the Breisgau S-Bahn from Hauptbahnhof Freiburg to Gottenheim/Breisach towards "Freiburg Messe/Universität".
• Option 2: Tram 4 direction "Messe"; Exit at the stop "Technische Fakultät" (see tram plan).

The mobile app of the local public transport company bwegt can also be very helpful to check the schedule of the trains and buses.

Tram tickets for local transport

Here you can find the types of tram tickets that VAG offers. The 2x4 rides ticket and the day pass are convenient options for several days and/or passengers.

Remote attendance

Hacking is not restricted to onsite, we appreciate your participation from anywhere else, too. We will have a Zoom room, open the whole 4 days, and involve a Meeting Owl to include you as close as possible.

Preliminary Schedule

The schedule is quite flexible: all days do not have a fixed end time (onsite decision with the participants). No requirement to join the whole week.

Monday, October 6th

Tuesday, October 7th

Wednesday, October 8th

Thursday, October 9th

Friday, October 10th

Social event optional. Sight seeing in Freiburg or visit to Mundenhof Tier Park.

Event rules and regulations

Code of Conduct

The Hackathon will abide the Galaxy Project CoC. Please, make sure that you read it before the event.

Data protection policy

This event follows the data protection policy established by the University of Freiburg as the host of the event. For details please refer to https://uni-freiburg.de/en/data-protection-applications/

Supporters

For any information contact Paul Zierep (email: zierep@informatik.uni-freiburg.de) or Bérénice Batut (email: berenice.batut@gmail.com)