SARS-CoV-2 whole genome sequencing

The course runs over 4 days in May 2021, starting Monday May​ 17th 2021 and ending Friday May 28th 2021.

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),

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


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.


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

To apply to the course follow this link.

Apply by May 10th 2021



(PDF document)​​

Links to Exercise surveys

Quiz 7Q

Exercise 9_10E

Exercise 12E​

Evaluation Survey

Please evaluate the course through this link:​ SARS-CoV-2 whole genome sequencing Evaluation


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