An introductory workshop on applied bioinformatic next-generation sequence analyses run by the National Bioinformatic Infrastructure Sweden (NBIS) in partnership with National Genomics Infrastructure (NGI).

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

02-Mar-2026 - 06-Mar-2026

Online only (Zoom)

This online training event is free of charge for academic participants subsidized by academic grants. The fee for non-academic participants is 12000 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.

INFO

Syllabus

Working on the unix/linux command line
- Command line navigation and related commands: cd, mkdir, rm, rmdir
- Commonly used linux tools: cp, mv, tar, less, more, head, tail, nano, grep, top, man
- Wildcards
- Ownership and permissions
- Symbolic links
- Piping commands
Working on remote computing cluster
- Logging on to a high performance compute cluster
- Booking resources
- Job templates, submission and queues
- Modules
Commonly used bioinformatic tools and pipelines
Working with integrated genome viewer
Variant-calling workflow
- Mapping reads to the reference genome
- Variant detection
- VCF file format
RNA-Seq workflow
- RNA-Seq experimental design and considerations
- QC, mapping and gene expression counts
- Differential gene expression analyses

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 organize 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

This workshop is open to PhD students, post-docs, and other researchers affiliated to Swedish academia and healthcare.

Required to be able to follow the tutorials:

BYOL, bring your own laptop configured according to precourse instructions.
A background in genetics, cell biology, biomedicine, biochemistry, bioinformatics or comparable.

To get the maximum benefit from the workshop:

Have a research project where you are currently using next generation sequencing or are planning to use next generation sequencing.

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. International applicants are accepted based on availability of seats

Credits & Certificate

Please note that NBIS training events do not provide any formal university credits. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not. Attendees with full attendance and completion of tasks will be issued a certificate of participation indicating topics covered and duration of the workshop.

REGISTRATION

Application form: https://nbis.typeform.com/ngsintro-2603
Application opens: 01-Dec-2025
Application closes: 30-Jan-2026
Decision: Few days after deadline

CONTACT

Diana Ekman, Martin Dahlö, Roy Francis
edu.intro-ngs [at] nbis.se

CODE OF CONDUCT

By participating in this workshop, you will be agreeing to the NBIS Code of Conduct.

2026 | National Bioinformatics Infrastructure Sweden