De novo Genome assembly, 1hp


National course hosted by BILS, a national resource for bioinformatics support. The course is open for PhD students, postdocs, researchers and other employees in need of bioinformatic skills within all Swedish universities.

Application form

Important dates

Application open: Beginning of September

Application deadline: October 7

Confirmation to accepted students: October 14

Responsible teachers: Henrik Lantz

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

Workshop fee

A workshop fee of 1000 SEK will be invoiced to accepted participants (includes the study material, coffee, lunches and course dinner).

Workshop content

The course is aimed at researchers getting into their first de novo genome assembly project, or those planning to do so in the near future, but will also include information of use for the more experienced researcher. The focus will be on eukaryotic organisms, but most of the methods can be applied to prokaryotic projects too. Applicants will be taken through all steps of a genome assembly project, from the quality assessment of data, through assembly, to validation of assemblies. After this course, the students will be well aware of common practices in genome assembly projects and will know how to avoid common pitfalls.

Topics covered will include:

  • Different sequencing technologies and their use in genome assembly
  • Quality assessment of data
  • Quality based cleaning and adapter trimming: needed or not
  • Assembly of genomes including overview of commonly used programs
  • Assembly validation

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 (e.g., transcriptome assembly, SNP calling) is a plus. Applicants are 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.