Introduction to bioinformatics using NGS data HT 2021
Title: Introduction to bioinformatics using NGS data HT 2021
SNIC Project: SNIC 2021/22-750
Project Type: SNIC Small Compute
Principal Investigator: Malin Larsson <>
Affiliation: Linköpings universitet
Duration: 2021-10-15 – 2022-01-01
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 November 22 and finishes on November 26 2021. It will be delivered online. Although the course is given from November 22 to 26 it would be good if we can have access to the SNIC project earlier so that we can prepare. We will use a singularity image with all the sofware and data required during the course, and it would be good if we have some time to properly test this. We will accept approximately 30 students to the course, and up to 8 teachers need to have access to the project so that they can test the computational exercises before.