Applied Bioinformatics
The aim of this course is to share how to use bioinformatics tools in a reproducible and scalable way. We will use environments, containers, and established pipelines so that you can run these analyses on any operating system, as well as on systems that are not high performance computing clusters. And first and foremost: these tools and techniques can be used regardless of which type of bioinformatics you are ultimately working with.
The website will remain active after the course so that you have access to the material even after the course.
We will meet in person in Ultuna between Monday, October 6th, and Friday, October 10th, 2025. However, to get the most out of this course, we expect you to do some preparation in advance. This is to set-up and get aquainted with some of the tools we will be using.
You will not be able to participate properly without completing the pre-course material! If possible start today and do a bit every day.
I want to thank Lizel Potgieter for her valuable contributions to the materials for this course!
Course content
before the course:
| Topic | Content |
|---|---|
| HPC access | Create user accounts for the HPC resources |
| VScode | Settting up and getting aquainted with VScode |
| Server access | SSH connect to the course server |
| Command line | Use the command line to manipulate data |
| screen | Manage persistent bash sessions |
| Quarto | Installing and using Quarto with VScode |
| git and GitHub | Version control with git and GitHub |
during the course:
| Day | Session |
|---|---|
| Monday | Welcome, introduction |
| Data Management & Reproducible Research | |
| Using git collaboratively | |
| Create a blog with Quarto | |
| Publish your blog with GitHub actions | |
| Tuesday | Introduction to environments |
| Quality control of sequencing data | |
| Bonus: Python in Pixi | |
| Introduction to containers | |
| Use containers | |
| Wednesday | nextflow |
| quality control with nextflow | |
| containers cont. | |
| Thursday | nf-core |
| Test a nf-core pipeline | |
| Set up a nf-core pipeline | |
| Friday | Visualize your results: ggplot |
| Discussion: AI in Bioinformatics | |
| clean-up and finishing |