SARS-CoV-2 whole genome sequencing

Recordings and Course material

This course is now freely available for self-learning. Presentations, Zoom recordings from the original course and course material to conduct the exercises have been combined and are available through the PDF file found below.

Please note that since this course is self-learning, we are not able to review your Analysis Report should you choose to conduct Exercise 9_10. We have however provided an Example report which you can use as a self-check and guide.

Course information

Title:

SARS-CoV-2 whole genome sequencing

Language of instruction:

English.

Offered as:

Webinar with lectures and exercises.

Duration of course:

4 x ½ days.

Responsible:

Rene S. Hendriksen (DTU), rshe@food.dtu.dk

Course co-responsible:

Pernille Nilsson (DTU), Anthony Smith (NICD, South Africa), Jinal Bhiman (NICD, South Africa), Marco van Zwetselaar (KCRI, Tanzania), Beverly Eygir (NMIMR, Ghana), Iruka N. Okeke (UI, Nigeria).

 

General course objectives:

The course introduces and cover all aspects of the entire WGS workflow for SARS-CoV-2 starting with a respiratory sample and finishing with completely analysed DNA sequence/genome.

The participant will upon completion of the course know all the steps included in preparing and conducting WGS using Illumina short read technology, which will include the wet laboratory procedures, computational genome assembly and the use of online tools to assess phylogenies and mutations in the global context.

Learning objectives:

A participant who has met the objectives of the course will be able to:

·Describe wet laboratory and computational workflow to generate and assemble SARS-CoV-2 genomes

·Perform wet laboratory protocols

·Perform drag-and-drop bioinformatics using online analysis tools and interpret the results

Content:

The course covers a detailed run through the sequencing workflow, starting with a respiratory sample to completed analysis of raw reads or assembled genome and will give the participants a thorough understanding of the process for short read technologies.

The course will comprise of lectures and hands-on exercises that the participants will have to complete and submit answers to in between course days.

Course literature:

No literature required. However, please find an overview of recommended reading below.

Audience:

Users with some experience/knowledge of WGS and WGS data (e.g. attended SEQAFRICAs Introduction to WGS in AMR surveillance)