Introduction to bioinformatics using NGS data

November 13, 2023 November 17, 2023


Navet, SciLifeLab Uppsala
SciLifeLab Uppsala, BMC C11, Husargatan 3
Uppsala, 75237 Sweden
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Introduction to bioinformatics using NGS data

November 13 @ 09:00 November 17 @ 17:00 CET

National workshop for PhD students, postdocs, researchers, and other employees within Swedish academia, introducing the analysis of next generation sequencing data.

The course is organized by: National Bioinformatics Infrastructure Sweden (NBIS) and National Genomics Infrastructure (NGI)

Responsible teachers: Malin Larsson, Martin Dahlö, Roy Francis

Contact information: 

Important dates

Application open: Jun 7, 2023

Application deadline: October 4, 2023

Confirmation to accepted participants: Week 41 (October 9-12)

Course fee

This on-site training event costs 3000 SEK for academic participants, invoiced to the participant’s organisation. If you accept a position and do not participate (no-show) you will still be invoiced 3000 SEK. Please note that NBIS cannot invoice individuals. We ask non-academic applicants to contact us regarding the fee. 

Course description

This intense one-week workshop provides 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 platforms and the advantages and challenges to using their data during the lectures. 

Course content

Briefly, the workshop covers the followings major topics:

  • Working on the UNIX/LINUX command line
  • Bioinformatic/NGS data formats and QC
  • DNA variant calling workflow essentials
  • RNA sequence analysis workflow essentials

Learning outcomes

After this workshop you should be able to:

  • Describe the basic principles of next generation sequencing.
  • Use the Linux command line interface to manage simple file processing operations, and organise directory structures.
  • Connect to and work on a remote high performance compute cluster.
  • Apply programs in Linux for analysis of NGS data.
  • Summarise the applications of current NGS technologies, including the weakness and strengths of the approaches and when it is appropriate to use which one of them.
  • Explain common NGS file formats.
  • Interpret quality control of NGS reads.
  • Explain the steps involved in variant calling using whole genome sequencing data.
  • Independently perform a basic variant calling workflow on example data.
  • Demonstrate hands-on experience with handling raw RNA sequencing data, QC and quantification of gene expression.
  • Explain the steps involved in differential gene expression using RNA seq data.

Entry requirements

To be able to follow the workshop you need to:

  • BYOL, bring your own laptop configured according to precourse instructions.
  • Have a background in genetics, cell biology, biomedicine, biochemistry, bioinformatics or comparable.
  • To get the maximum benefit from the workshop you should:
  • Have a research project where you are currently using or are planning to use next generation sequencing.

Selection criteria

Due to limited space the course can accommodate a maximum of 30 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the workshop as well as gender and geographical balance. Priority is given to PhD scholars followed by other researchers, and we will prioritise applications  from Swedish academia.

SciLifeLab Uppsala, BMC C11, Husargatan 3
Uppsala, 75237 Sweden
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Last updated: 2023-06-07

Content Responsible: Maria Bäckström(