Metagenomics, 1 hp

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


Application page

Important dates

Application open: August 1

Application deadline: October 7
We will also consider late registrations from qualified applicants.

Confirmation to accepted students: October 20

Responsible teachers: Thijs Ettema, Anders Andersson, Moritz Buck

If you don’t receive information according to the dates above, contact

Course fee

A course fee of 1300 SEK will be invoiced to accepted participants (includes coffee, lunches and course dinner). NOTE – Uppsala University cannot invoice individuals.

Course content

During the three-day SciLifeLab metagenomics course, the participants will be brought up to date with the current state-of-the-art in the rapidly emerging field of environmental genomics, including metagenomics and single cell genomics. The course will focus on computational methods for assembly and functional annotation of environmental genomics data.

Topics covered will include:

  • Quality assessment of sequence reads
  • Assembly of metagenomic and single cell genomic datasets
  • Gene calling and functional annotation – different binning strategies for metagenomics contigs
  • Comparative metagenomics

Entry requirements

Participants must be comfortable navigating a linux shell and execute programs from the command line. Without this knowledge, it will be impossible to participate in the computer exercises. Previous experience from working with NGS data (genome assembly, transcriptome assembly, SNP calling) is a plus. Applicants are also encouraged to bring their own laptops, but there will be computers to use for participants unable to do so.

Due to space constraints for the computer exercises, there are a maximum number of allowed participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance.