Workshop

The chapters in this section of the site will lead you through each step of the workshop. Please work through these steps in order and, if you get stuck, please ask one of the lecturers or demonstrators for help.

  1. Log in to your account at https://usegalaxy.eu/
  2. Download the workshop data to your computer
  3. Upload the workshop data to your Galaxy history
  4. Prepare your sequencing read data for assembly
  5. Assemble a genome from your sequencing data
  6. Visualise your genome assembly
  7. Annotate your assembly
  8. Visualise your annotation
  9. Map reads from your SARS-CoV-2 isolate to the SARS 2003 genome
  10. Visualise the mapped reads using JBrowse2
  11. Identify sequence variants (SNPs, Single Nucleotide Polymorphisms) between SARS-CoV-2 and SARS 2003
  12. Use what you’ve learned to identify and interpret changes in the SARS-CoV-2 virus during the COVID-19 pandemic