Introduction to bioinformatics using NGS data HT 2020
Title: Introduction to bioinformatics using NGS data HT 2020
SNIC Project: SNIC 2020/13-57
Project Type: SNIC Small Compute
Principal Investigator: Malin Larsson <>
Affiliation: Linköpings universitet
Duration: 2020-09-01 – 2020-12-01
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 9 and finishes on November 13. It will be given in Uppsala, unless we need to move it online due to the current corona situation. We give this course several times each year and alternate the venue between different Swedish universities, but this particular application is for the course in Uppsala in November 2020. Although the course is given from November 9 to 13, 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, since this is the first time we will use resources at NSC (if we are approved) it would be good if the project could start a few months earlier than November 9 so that we have time to test our exercises and the singularity image that we will create for the course. It would be very good if the project could be active during September, October and November 2020. 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 computational exercises before. If we can reserv compute cores during the period from November 9 to November 13 it would be great. If so we need one core per student from 9 am to 5 pm during these days.