Introduction to bioinformatics using NGS data VT 2023
Title: Introduction to bioinformatics using NGS data VT 2023
DNr: SNIC 2022/22-1169
Project Type: SNIC Small Compute
Principal Investigator: Malin Larsson <>
Affiliation: Linköpings universitet
Duration: 2023-01-10 – 2023-04-01
Classification: 10203


This is an intense one-week PhD course in bioinformatics providing an introduction to the analysis of next generation sequencing data. Lectures on the theory of concepts will be paired with practical computational exercises in the Linux environment. The practical exercises will focus on data from the Illumina platform, but we will discuss other sequencing technologies and the advantages and challenges to using their data during the lectures. Topics covered will include: • Introduction to Linux and HPC computing • NGS read-to-reference alignment • Genetic variant calling in populations • RNA-Seq expression analysis This is a national course with students from all over Sweden. It is organized jointly by SciLifeLab ( and National Bioinformatics Infrastructure Sweden ( Responsible teachers are Malin Larsson (Linköping University), Martin Dahlö (Uppsala University) and Roy Francis (Uppsala University). The course starts on February 6 and finishes on February 10 2023. It will be a hybrid course with classrooms in Uppsala, Umeå and Lund. It would be good if we can have access to the SNIC project about a month before the start of the workshop and a few weeks after, to give us time to prepare. We will use a singularity image with all the software and data required during the course, and it would be good if we have some time to properly test this. We will accept approximately 60 students to the course, and up to 10 teachers need to have access to the project so that they can test the computational exercises before.