De Novo Genome assembly


National course open for PhD students, postdocs, researchers and other employees in need of genome assembly skills within all Swedish universities.

The course is run by the SciLifeLab bioinformatics platform NBIS (https://www.nbis.se).

Apply here

Important dates

Application closes: October 15

Confirmation to accepted students:  October 22

Responsible teachers:  Henrik Lantz

If you do not receive information according to the above dates please contact:  henrik.lantz@nbis.se

Course fee

A course fee* of 1700 SEK will be invoiced to accepted participants. This includes lunches, coffee and snacks.

*Please note that NBIS cannot invoice individuals

Course content

The course is mostly aimed at researchers getting into their first de novo genome assembly project, but will also include information of use for the more experienced researcher. We will cover assembly of both prokaryotes and eukaryotes and spend a lot of time on learning how to run the analyses in hands-on computer exercises. 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, including Illumina, PacBio, Oxford Nanopore, 10X Genomics, and Hi-C data
  • Quality assessment of data
  • Data filtering including Quality based cleaning and adapter trimming
  • Assembly of genomes including overview of commonly used programs
  • Assembly validation and polishing
  • Contamination analyses

Entry requirements

This is an advanced course. Participants must be comfortable navigating a Linux shell and executing 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 is beneficial. Applicants are encouraged to bring their own laptops, but there will be computers to use for participants unable to do so.

Due to limited space the course can accommodate a maximum of 14 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.