WGS workflow - from isolate to analysis

The course originally ran over 4 days in March 2021, starting Monday 22 March 2021, and ending Monday 29 March 2021.​

​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 provide feedback on work submitted for the exercises beyond the automated response to certain questions.

Start your self learning here:

   Course Material

Disclaimer: ​The course material is not be used for commercial purposes.

Please also note that the rapid development of sequencing technology might cause

certain information to be incomplete.

Course information

Title: WGS workflow: from isolate to analysis.

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 starting with a bacterial isolate and finishing with completely analysed DNA sequence/genome.

The participant will upon completion of the course i) know all the steps included in preparing and conducting WGS using Illumina short read technology and ii) similarly know the steps included in preparing and conducting long read sequencing using the MinIon from Oxford Nanopore Technologies (ONT).

Learning objectives:

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

·​Describe the sequencing workflow for both short read (Illumina) and long read (ONT) technologies.

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

·​Be familiar with data sharing practises and the most common public repositories and know how to submit data to them.


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

Material and Agenda from original course in 2021​


(PDF document)​​

Links to exercise surveys

​Exercise [2E]

Exercise [5E]

Exercise [9E]

Evaluation Survey

Please evaluate the course through this link:​ WGS workflow - from isolate to analysis Evaluation


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