Structure

In total, the course is designed to take 2 weeks of face time. The course is designed as an instructor led course  with the following components:

Theme 1:

  • Intro, Getting started with programming (UNIX/python): 2 days 

Theme 2:

  • Wetlab protocols, sequencing technologies (Illumina, nanopore), raw-data QC: 1 day 
  • Genome assembly (de novo: short-read, long-read and hybrid) and QC: 1,5 days  
Theme 3:
  • Genome analysis (blast, in silicone MLST, annotation, phylogenetics, lineage assignment, outbreak analysis, AMR ): 2,5days
  • Data sharing (Public repositories, ECDC toolbox): 1 day 
Theme 4:
  • Pipeline development/automation: 1 day 
  • Large-scale automation (incl. site-visit), further learning/resources, wrapping up and course evaluation: 0,5 day

Theme 5:

  • How to keep learning, Q and A with course trainers: 0,5 day


Last modified: Wednesday, 24 April 2024, 1:38 PM