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
  

18-Mar-2024 - 22-Mar-2024

Online only (Zoom)

This online training event has no fee. However, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 3000 SEK. 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 UPPMAX
  • 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

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

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

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/to/FtyPJpN8 Links to an external site.
Application opens:  04-Dec-2023
Application closes: 05-Feb-2024
Confirmation of acceptance:  Week 6, 2024

CONTACT

Malin Larsson, 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.

2024 | National Bioinformatics Infrastructure Sweden