SciLifeLab workshops, Uppsala, in collaboration with BILS


Workshop 1: De Novo Genome Sequencing and Annotation, 26th-27th November
Workshop 2: Metagenomics, 28th-29th November

Responsible teacher: Henrik Lantz

Applicants are welcome to apply to one or both of the workshops. As the two workshops are meant to stand on their own, there is some over-lap, in particular for quality assessment of reads and gene calling.

Entry requirements for both workshops:

Required – Basic knowledge of Linux command line, including how to navigate file systems and how to run programs

Recommended – Experience of Next Generation Sequencing data, e.g., genomic reads or RNA-seq.

De Novo Genome Sequencing and Annotation, 26th-27th Nov.

Course content:

The course is aimed at researchers getting into their first de novo genome 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 and validation of assemblies, to annotation of assembled genomes. 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
  • Gene prediction
  • Protein alignment
  • Genome browsers

Metagenomics, 28th-29th Nov.

Course content:

During the two-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

General information

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

Responsible teacher: Henrik Lantz

Application form

Important dates:

Application open: September 23rd
Application deadline: October 28th
Confirmation to accepted students: November 1st

If you don’t receive information according to the dates above, contact: henrik.lantz@imbim.uu.se

Course fee

A course fee of 1000 SEK for one workshop (1800 SEK for both) will be invoiced to accepted participants (includes the study material, coffee, lunches and course dinners).

Organizer: SciLifeLab