WGS workflow - from isolate to analysis

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.

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.

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).
• 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.

Content

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 is comprised of lectures and hands-on exercises that the participants complete on their own. Self-evaluation is possible through responding to surveys related to the exercises.

No literature required.

Audience

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

 

Day 1: Monday – 22 March 2021 – Sequencing workflow

Speaker/ Presenter	Content	Slides/Video/ Exercise sub
	Entire day 1 training: incl. Welcome, Introduction, and wrap-up	Slides/Video
Anderson Oaikhena (University of Ibadan, Nigeria)	[1] Introducing the workflow: Going from bacterial isolate to Genome – Synopsis of all the steps.	Slides/Video
Shannon Williams (NICD, South Africa)	[2] DNA isolation: From bacterial culture to high quality DNA.  Different methods will be presented covering commercial kits and automated DNA extraction systems. Additional short videos:  [2b] Magcore Automated DNA extraction [2c] Qiagen Overview [2d] Qiagen DNeasy protocol [2e] Nanodrop Spectrophotometer [2f] Qubit Fluorometer	Video
Shannon Williams (NICD, South Africa) & Beverly Egyir (NMIMR, Ghana)	[2E] Exercise: Investigating quality checks on isolated DNA.   You will perform the exercise on your own computer and can test your knowledge by taking the quiz to to self-evaluate.	PDF/Slides/Quiz

Day 2: Wednesday – 24 March – Illumina and ONT sequencing

	Day 2 training: incl. Welcome, Introduction, Q&A and wrap-up	Slides/Video*
Happiness Kumburu                    (KCRI, Tanzania)	[3] Illumina library prep: Going from high quality DNA to sequencing libraries.	Slides
Happiness Kumburu (KCRI, Tanzania)	[4] Illumina sequencing: Hands-on how to load the machine with your prepared libraries.	Video
Stanford Kwenda (NICD, South Africa)	[5] Downloading data: Once the sequencing run is finished, how do you get your data? (Pre-recorded video / Demonstration)	Slides/Video
Pernille Nilsson (DTU, Denmark)	[5E] Exercise: Introduction to an exercise to recap QC of sequence output.  You will perform the exercise on your own computer and can test your knowledge by taking the quiz to to self-evaluate.	Video/ Tutorial/ Files Quiz

* Recording of the Introduction to Nanopore sequencing has been edited out. Up to date introductory videos on ONT technology and much more is available on the ONT website and on the ONT YouTube channel.

Day 3: Friday – 26 March – Recap Bioinformatics, BIGSdb, EnteroBase and protocols

	Day 3 training: incl. Welcome, Introduction and Q&A	Slides/Video*
Marco van Zwetselaar               (KCRI, Tanzania)	[7] Recap on bioinformatics: FASTQ, fasta; assembly, mapping, kmer counting, and why do we do it?	Slides/Video
Marco van Zwetselaar (KCRI, Tanzania)	[8] Recap on CGE tools: Refreshing the knowledge on available online tools	Slides/Video
Anthony Smith (NICD, South Africa)	[9] Introduction to BIGSdb and EnteroBase: Demonstration of data analysis at EnteroBase.	Video
Anthony Smith (NICD, South Africa)	[9E] Exercise: Introduction to an exercise using EnteroBase	Slides
Jette Sejer Kjeldgaard (DTU, Denmark)	[10] Protocols and ISOs	Slides

* Some of the recording is missing (introduction to [9E] and [10]) due to technical issues during zoom recording.

Day 4: Monday – 29 March – Data sharing

	Entire day 4 training: incl. Welcome, Introduction, Q&A and wrap-up	Slides/Video
Tolbert Sonda/                          Marco van Zwetselaar (KCRI, Tanzania) & Ayorinde Afolayan (UI, Nigeria)	[11] Data sharing practices and repositories: Introducing how and where to make raw sequencing data and assembled genomes publicly available. GenBank (NCBI, ENA, Enterobase etc.)	Slides/Video Slides/Video Video
Shannon Williams (NICD, South Africa), Beverly Egyir (NMIMR, Ghana), Pernille Nilsson (DTU, Denmark) & Anthony Smith (NICD, South Africa)	Going through results from all exercises	Video
Pernille Nilsson (DTU, Denmark)	Concluding remarks and close.