Oldenburg workshop - April 2026
Table of Contents
This event is in the past. If you are interested in attending a similar workshop, feel free to inquire with us about the next planned event.
We are planning a free, in-person workshop and early-career researcher symposium to discuss integrated microbial ‘omics and learn how to use anvi’o. The topics that we will cover during the workshop include,
- Genomics
- Metagenomics
- Genome-resolved metagenomics
- Microbial metabolism
- Pangenomics
- Phylogenomics
If you are interested in attending, please consider applying as soon as possible as we have limited number of seats in the workshop venue, and mark your calendars for April 13-17, 2026.
Do you know someone who may be interested in attending? Please feel free to share this page with them!
Please find photos and the outcomes of a previous iteration of the same workshop here.
An important note on funding. While the workshop itself is free (with lunch and coffee provided), we unfortunately do not have the funds to cover travel and accommodation costs for participants. That said, we are currently seeking funds to support the travel needs of at least some participants who may not be able to attend the event without it. Thus, we strongly encourage applications from institutions with limited resources around the globe. Please indicate in your application if you will need travel support. If we are able to acquire funding, we will likely be able to support a few of these applications. Feel free to write to any of us if you have any questions.
The flyer for the workshop.
When and Where
From April 13, 2026 (Monday) to April 17, 2026 (Friday) at the Helmholtz Institute for Functional Marine Biodiversity (HIFMB) in Oldenburg, Germany. Here is a map for you:
Program
In addition to intense hands-on training sessions, this event includes an ECR symposium, during which all of the participants will give lightning talks about their research. We will send the details of lightning talks to each participant upon their invitation.
Here is an overview of the workshop content:
Monday 13: Genomics
| 9:00 - 9:15 | Introduction to the workshop faculty, program & setting |
| 9:15 - 10:15 | Introduction to the anvi’o software ecosystem |
| 10:15 - 10:30 | Coffee & Tea Break |
| 10:30 - 12:00 | The anvi’o interactive interface |
| 12:00 - 13:00 | Group lunch (on-site, vegan/vegetarian food) |
| 13:00 - 14:00 | Symposium talks |
| 14:00 - 15:30 | Genomics (gene calling, functional annotation, taxonomic characterization) – tutorial |
| 15:30 - 15:45 | Coffee & Tea Break |
| 15:45 - 17:30 | Genomics – tutorial, continued |
Tuesday 14: Pangenomics; Phylogenomics
| 9:00 - 10:15 | Pangenomics (comparing gene content across genomes) – theory |
| 10:15 - 10:30 | Coffee & Tea Break |
| 10:30 - 12:00 | Pangenomics – tutorial |
| 12:00 - 13:00 | Group lunch (on-site, vegan/vegetarian food) |
| 13:00 - 14:00 | Symposium talks |
| 14:00 - 15:30 | Pangenomics – tutorial, continued |
| 15:30 - 15:45 | Coffee & Tea Break |
| 15:45 - 17:30 | Phylogenomics (estimating evolutionary relationships) – theory + tutorial |
Wednesday 15: Metabolism
| 9:00 - 10:15 | Metabolism estimation (from individual genes to pathways) – theory + tutorial |
| 10:15 - 10:30 | Coffee & Tea Break |
| 10:30 - 12:00 | Metabolism estimation – tutorial, continued |
| 12:00 - 13:00 | Group lunch (on-site, vegan/vegetarian food) |
| 13:00 - 14:45 | Reaction networks and metabolic interactions – tutorial |
| 14:45 - 15:00 | Coffee & Tea Break |
| 15:00 - 17:30 | Free time for work, rest, and/or social activities |
Thursday 16: Metagenomics
| 9:00 - 10:15 | Metagenomic read recruitment (detecting genes/genomes across samples) – theory + tutorial |
| 10:15 - 10:30 | Coffee & Tea Break |
| 10:30 - 12:00 | Metagenomic read recruitment – tutorial, continued |
| 12:00 - 13:00 | Group lunch (on-site, vegan/vegetarian food) |
| 13:00 - 14:00 | Symposium talks |
| 14:00 - 15:30 | Genome-resolved metagenomics (best practices in genome binning and refinement) – tutorial |
| 15:30 - 15:45 | Coffee & Tea Break |
| 15:45 - 17:30 | Genome-resolved metagenomics – tutorial, continued |
Friday 17: Scalable bioinformatics
| 9:00 - 10:15 | How to use automated, scalable, and reproducible bioinformatics workflows – tutorial |
| 10:15 - 10:30 | Coffee & Tea Break |
| 10:30 - 12:00 | Bioinformatics workflows – tutorial, continued |
| 12:00 - 13:00 | Group lunch (on-site, vegan/vegetarian food) |
| 13:00 - 14:00 | Symposium talks |
| 14:00 - 15:30 | Bioinformatics workflows – tutorial, continued |
| 15:30 - 15:45 | Coffee & Tea Break |
| 15:45 - 17:30 | Bioinformatics workflows – tutorial, continued |
Workshop materials
The lecture slides for the workshop can be downloaded from this Figshare link.
The table below shows the links to the tutorials used in each workshop session.
| Monday | Interactive interface | https://anvio.org/tutorials/interactive-interface/ |
| Monday | Genomics | https://anvio.org/tutorials/trichodesmium-tutorial/ |
| Tuesday | Pangenomics | https://anvio.org/tutorials/trichodesmium-tutorial/chapter-2 |
| Tuesday | Phylogenomics | https://anvio.org/tutorials/trichodesmium-tutorial/chapter-3 |
| Wednesday | Metabolism | https://anvio.org/tutorials/trichodesmium-tutorial/chapter-4 |
| Thursday | Metagenomic read recruitment | https://merenlab.org/tutorials/read-recruitment/ |
| Thursday | Metagenomic binning | https://merenlab.org/tutorials/infant-gut/#chapter-i-genome-resolved-metagenomics and https://anvio.org/tutorials/binning-popgen-oral-microbiome |
| Friday | Workflows | https://anvio.org/tutorials/scaling-up/ |
How much does it cost?
There is no fee to attend the workshop, and we will cover your lunches and coffee/tea breaks. The rest is up to you.
If you do not have the funds to support your own travel and accommodation, please consider applying anyway. You should indicate in your application that you need travel support. If we are able to acquire funding to help us pay for participant travel, then we will happily consider your application.
Registration
The application deadline was on December 10, 2025.
List of Faculty
The following individuals from the HIFMB were responsible for organizing and teaching the workshop.
| Name | Role |
|---|---|
 |
Primary Organizer & Faculty |
 |
Primary Organizer & Faculty |
 |
Organizer & Faculty |
 |
Teaching Assistant |
 |
Teaching Assistant |
| Avril von Hoyningen-Huene | Teaching Assistant |
List of Participants
The following 39 individuals attended the workshop.
Full Name |
University / Institution |
|---|---|
| Adam Jenofalvi | Biosustain, Technical University of Denmark |
| Adam Vivian-Smith | Forest Genetics and Regeneration, Norwegian Institute of Bioeconomy Research |
| Ahmad Hafiz Adeel | Institute of Soil Biology and Biogeochemistry, Biology Centre CAS |
| Ana Maria Ramos Arroyo | Department of Biochemistry, School of Medicine, University of Costa Rica |
| Anna Tausch | ICBM, University of Oldenburg |
| Arlie McCarthy | University of Oldenburg |
| Bram Vekeman | Department of Microbial Ecology, University of Vienna |
| Carina Bunse | Department of Marine Sciences, University of Gothenburg |
| Charlotte Kunze | Helmholtz Institute for Functional Marine Biodiversity |
| Chloe Economou | Biologicals, Syngenta |
| Christiane Böckel | Helmholtz Institute for Functional Marine Biodiversity |
| Clara Maria Arboleda Baena | German Centre for Integrative Biodiversity Research (iDiv) |
| Ella Case | Biology/Chemistry, MARUM, University of Bremen |
| Esma Nur Bozlak | Environment, Earth & Ecosystem Sciences, The Open University |
| Eva Donini | Department of Pharmacy and Biotechnology, University of Bologna |
| Gurpreet Kharey | Biological Sciences, University of Calgary |
| Igor Oliveira Duarte | Zoology Institute, University of Kiel |
| Isabela Nori Ruscito | Department of Biological Oceanography, Oceanographic Institute, University of São Paulo |
| Isha Athale | ICBM, University of Oldenburg |
| Julia Pamphile dos Santos | MARUM, University of Bremen |
| Kaumudi Prabhakara | Microbial Population Biology, Max Planck Institute for Evolutionary Biology |
| Krzysztof T. Jurdzinski | Gene Technology, KTH Royal Institute of Technology |
| Kuldeep Dilip More | The Geological Survey of Denmark and Greenland |
| Maia El Zahab | ICBM, University of Oldenburg |
| Maria Papadatou | Department of Functional and Evolutionary Ecology, University of Vienna |
| Mona Parizadeh | Cumming School of Medicine, University of Calgary |
| Nicolai Verbücheln | Department of Marine Sciences, University of Gothenburg |
| Nina Tölke | Institute of Earth Surface Dynamics, University of Lausanne |
| Nithin Joseph Simon | University of Oldenburg |
| Or Amar | University of Amsterdam |
| Pegah Kalatehjari | Department of Microbial Ecology and Environmental System Science, University of Vienna |
| Sadaf Khan | Department of Agroecology, Aarhus University |
| Sarah Förster | DOME: Centre for Microbiology and Environmental Systems Science, University of Vienna |
| Sarah Hahnke | Helmholtz Institute for Functional Marine Biodiversity |
| Sergio George | Pediatrics, Universidad de Chile / Genetics, University Medical Center Groningen |
| Slimane Khayi | Microbiology, Institut National de la Recherche Agronomique (INRA) |
| Sophia Fatima | Max Planck Institute for Marine Microbiology |
| Tomasa Sbaffi | Water Research Institute, National Research Council of Italy |
| Vitória da Silva Pereira Domingues | Federal University of Rio de Janeiro |