De novo Genome Assembly, 1 hp


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

 

Important dates

Application open: June 19

The course has a few open spots left for qualified applicants.
To inquire about open spots, please contact education@scilifelab.uu.se

Confirmation to on-time accepted students: October 9
For late applicants, we aim to give you a response within one week.

Responsible teacher: Henrik Lantz

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

Course fee

A course fee of 1300 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 website

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 (see our sister course in metagenomics for assembly of mixed/environmental samples) 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 and PacBio data
  • Quality assessment of data
  • Quality based cleaning and adapter trimming
  • Assembly of genomes including overview of commonly used programs
  • Assembly validation
  • 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 (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 is 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.