Oldenburg workshop - April 2026
Table of Contents
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.
Applications to this event are now closed. The application deadline was on Dec 10, 2025.
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
We will update this section with a link to download slides after the workshop. Tutorial links will also be updated before the workshop begins.
The table below shows the links to the tutorials used in each workshop session.
| Monday | Interactive interface | TBD |
| 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 are responsible for organizing and teaching the workshop.
| Name | Role |
|---|---|
 |
Primary Organizer & Faculty |
 |
Primary Organizer & Faculty |
 |
Organizer & Faculty |
List of Participants
We will update this section with a list of all participants after the workshop.