National course. The course is open for PhD students (prioritized), postdocs, researchers and other employees in need of bioinformatic skills within all Swedish universities.

The course is run in collaboration with the Bioinformatics Core Facility at the University of Gothenburg.

Application page

Important dates

Application open: January 18, 2017

Application deadline: April 5, 2017

Confirmation to accepted students: April 12, 2017

Responsible teachers: Manfred Grabherr, Magnus Alm Rosenblad

If you don’t receive information according to the dates above, contact education@scilifelab.uu.se

Course fee

A course fee of 1800 SEK will be invoiced to accepted participants (includes the study material, coffee, lunches and course dinner). NOTE – Uppsala University cannot invoice individuals.

Course content

Course webpage

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
• Data management

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.

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.