Introduction to bioinformatics using NGS data – ONLINE
Date: 24 - 28 March 2025
Timezone: Stockholm
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
Selection criteria
If we receive more applications than we have seats in the course, 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.
Responsible teachers: Malin Larsson, Martin Dahlö, Roy Francis
Important dates
Application opens: 13-Jan-2025
Application closes: 23-Feb-2025
Confirmation to accepted students: Week 9, 2025
Course fee
This online training event is subsidized by academic grants and thereby free of charge for academic participants. The fee for non-academic participants is 12 000 SEK.
Non-show fee: If you accept a position at the workshop but fail to attend without a valid reason (sickness or urgent family matter), you will be liable for a now-show fee of 3000 SEK (for academic participants) or the full fee (for non-academic participants).
Please note that NBIS cannot invoice individuals.
Contact: edu.intro-ngs@nbis.se
Keywords: bioinformatics, NGS
Venue: Online
City: Online
Country: Sweden
Prerequisites:
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.
Learning objectives:
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.
Target audience: PhD Students, postdocs, researchers, everyone, industry professionals
Event types:
- Workshops and courses
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