Introduction to bioinformatics using NGS data VT 2021
Title: Introduction to bioinformatics using NGS data VT 2021
SNIC Project: SNIC 2021/22-101
Project Type: SNIC Small Compute
Principal Investigator: Malin Larsson <>
Affiliation: Linköpings universitet
Duration: 2021-04-01 – 2021-07-01
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 May 17 and finishes on May 21. The course will be given online. We give this course two times each year and alternate the venue between different Swedish universities, but due to the Covid-19 situation this time it will be given online. Although the course is given from May 17 to May 21, it would be good if the students can go back and work on the computational exercises on their own for a short period after the course has finished. Also, it would be good if the project could start a few weeks earlier than May 17 so that we have time to test the labs and the singularity image that we have created for the course. It would be very good if the project could be active during April, May and June 2021. We will accept approximately 25 students to the course, and up to 8 teachers need to have access to the project so that they can test the exercises beforehand.