BM425 Workshop 1: SARS-CoV-2 Genome Analysis

Author

Leighton Pritchard and Morgan Feeney

Published

September 27, 2024

Preface to 2024-25 BM425 Workshop 1

Welcome to the BM425 (Advanced Microbiology) workshop on SARS-CoV-2 genome analysis, for 2024-25.

This year is the first presentation of the workshop material in this format, and we would be very grateful to hear feedback by email or through the GitHub repository Issues page.

Overview

This workshop asks you to work through some bioinformatics exercises using the online service Galaxy, with data that we provide, to:

  • assemble, annotate, and visualise the first SARS-CoV-2 genome isolated in Wuhan, in January 2020
  • compare the genome of SARS-CoV-2 to that of an earlier coronavirus (SARS 2003)
  • compare the genome of the first SARS-CoV-2 genome to that of an variant from later in the pandemic
  • make a biological interpretation of your analysis, particularly of the spike (S) protein
Important Note

There is new material in this workshop that is not covered in lectures. This material is examinable.

Please take care to read the text in the expandable callout boxes, as well as that for the workshop activities, to be sure you have understood the topic and obtain full value from the exercises.

How To Move Through These Workshop Materials

On your first run through this workshop, you should read each page in turn, and carry out each activity. You can see what activities are involved in the navigation sidebar on the left hand side of this page.

As you complete each activity, you can use the arrows at the bottom of the page to move forward and backward. If you need to, you can use the navigation sidebar on the left to jump to a section, and you can use the search field at the top of the sidebar to find specific content.

Please work through the workshop steps in order and, if you get stuck, please ask one of the lecturers or demonstrators for help.

  1. Join the training session at https://usegalaxy.eu/join-training/bm425-workshop1-2024
  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

Learning Objectives

By the end of this workshop, students will be able to:

  • understand and use the Galaxy scientific workflow system (Galaxy Community (2024))
  • recognise and use common sequencing data formats
  • use common bioinformatics tools to:
    • assemble sequenced reads into a genome sequence
    • annotate features on an assembled genome sequence
    • map sequencing reads onto an assembled genome
    • carry out comparative genome analysis
    • visualise and interpret the results of genome annotation and analysis

Assessment

Important

There is a formative assessment on the workshop MyPlace page that you should complete at the end of the workshop, to demonstrate you’ve earned your genomics wings (link below).