PhD - Medical science
(SS 2025)
Introduction to Next Generation Sequencing data analysis
Lecturer
- Stefan Coassin , PhD
- Sebastian Schönherr , Dr.techn.
Overall Aim
This course provides students with essential knowledge in Genetics and Computational Biology to conduct genetic analyses and interpret results effectively. The goal is to offer insights into both fields and provide a structured approach for large-scale genetic studies. The class is structured with a 70% focus on computational methods and a 30% focus on biology.
Date and Time
The course runs from March 17th to March 21st, 2025, from 10:15 AM to 5:00 PM in Computer Room C3, Fritz Pregl Strasse 3 (1st floor). On Monday, the Linux Crash Course starts at 11:15 AM.
Content
- Introduction to Linux & the Command Line (Optional)
- Introduction on second generation (Illumina, IonTorrent) and third generation sequencing technologies
- A standard NGS Data Processing Pipeline (DNA) on the command line
- Introduction to Github and Reproducibility of Pipelines
- Scripting
- Variant Calling Pipelines with the Nextflow Workflow Manager & SLURM
- Bioinformatics predicts variant effects by analyzing DNA and RNA data in downstream applications.
Hackathon
The hackathon takes place on the last day of the class, providing an opportunity to apply newly learned skills to predefined projects.
IMPORTANT:
Basic Linux knowledge is required. If you are not familiar with Linux, a foundational Linux session will be held on the first day (Monday). Participants are encouraged to contact sebastian.schoenherr@i-med.ac.at in advance for additional preparation and guidance before the course begins.
Repository
Class repository with exercises can be found here.