Introduction to Bioinformatics using NGS data, Uppsala


National course. The course is open for current and potential facility users such as PhD students, postdocs, group leaders and core facility staff in need of bioinformatic skills within all Swedish universities.

This course is supported by SciLifeLab and run by the SciLifeLab National Bioinformatics Infrastructure Sweden (NBIS).

Important dates

Application opens: April 25

Application deadline: June 11

Confirmation to accepted participants: June 14

Responsible teachers: Manfred Grabherr

If you don’t receive information about your application before June 18, contact education@scilifelab.uu.se

Social program

The course contains a voluntary social program for networking purposes (includes the coffee, lunches and one course dinner with teaching experts). A course fee of 1800 SEK will be invoiced to accepted participants that attend the social program, after completion of the course.
NOTE – Uppsala University cannot invoice individuals.

Course content

For schedule and pre-course information, please see https://scilifelab.github.io/courses/ngsintro/1902/

The course will provide an entry-level introduction to a wide range of analytical techniques for massively parallel sequencing, including basic Linux commands. We will pair lectures on the theory of analysis algorithms with practical computational exercises demonstrating the use of common tools for analyzing data from each of several common sequencing study designs.

Topics covered will include:

  • Basic Linux usage
  • NGS read-to-reference alignment (genomic and RNA-Seq)
  • Variant calling in populations
  • De novo assembly of RNA-sequence data
  • Reference-guided RNA-Seq expression analysis

Analysis techniques covered will focus mostly on data from the Illumina platform, but we will discuss other sequencing platforms and the advantages and challenges to using their data.

Please note that SciLifeLab training courses do not provide any formal university credits.
The course content is estimated to correspond to 
a certain number of credits, however the estimated credits are just guidelines.
If formal credits are crucial, the student needs to confer with the home department before course application, whether the course is valid for formal credits or not.

Entry requirements

  • A background in genetics, cell biology, biomedicine, biochemistry, bioinformatics or comparable is desirable

To get the maximum benefit from the course we would like you to

  • Have relevant previous experience in sequencing or analysis
  • Have a research project where you are currently using next generation sequencing or are planning to use next generation sequencing
  • Be able to bring your own laptop for the practical computational exercises
  • It is beneficial if you are directly performing analyses or if you have a support role and will be able to participate in a wide range of projects and transfer your knowledge to others

Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance.