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A Practical Guide for SARS-CoV-2 Whole Genome Sequencing

Learn the fundamentals of viral sequencing, sequencing library preparation, and SARS-CoV-2 sequencing best practices.

2,740 enrolled on this course

A hand holding a experiment tube with a DNA sequence in the background
  • Duration

    3 weeks
  • Weekly study

    5 hours
  • Digital upgrade


Strengthen your knowledge of genomics surveillance approaches

Accurate sequencing information is required to inform evidence-based public health decisions to tackle infectious diseases and pandemics such as COVID-19. This course highlights all of the relevant steps needed for processing, sequencing, and analysing viral samples.

This three-week course will provide tools and resources for capacity building aiming to strengthen genomics surveillance approaches.

Investigate SARS-CoV-2 sequencing methodologies

Using research, articles, and videos, you will access information and techniques to optimise your current data handling and processing.

You will learn about sequencing platforms and library preparation methodologies, comparing the benefits and limitations of each approach and its associated protocols.

Apply data quality control and analysis

With an introduction to data quality control metrics and standards, you will learn how to interpret high-quality data and how to perform basic viral genetic diversity analyses.

You will learn how to process and report on your quality control and also the ethical considerations of genomic sequencing.

Contribute to the global response to COVID-19

Once equipped with the skills to gather and analyse your data, you will be able to discuss and plan the most appropriate strategy for your team.

You will gain an overview of how global experts overcame the challenges to tackle a pandemic and how you can apply these experiences to other global health threats.

You will finish this course understanding the entire process of viral sequencing, able to make vital contributions to the development of pathogen genomics capacity in a global context.

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Skip to 0 minutes and 15 seconds Welcome to the course “A Practical Guide For SARS-CoV-2 Whole-Genome Sequencing”. In this three week course, you will learn the basic concepts of viral sequencing, sequencing library preparation, and how to apply SARS-CoV-2 sequencing best practises. You will learn about different sequencing platforms and library preparation methodologies. And you will compare their benefits and limitations. You will also learn about sample and data quality control metrics and standards. Together, we will investigate high throughput approaches for sequence generation. And understand how to interpret the output of sequence data pipelines. In this course, you will also learn how to identify ways to scale up SARS-CoV-2 sequencing.

Skip to 0 minutes and 59 seconds Towards the end of the course, you will learn about sequence analysis, variant classification, and other aspects such as quality control reporting and ethical considerations. The entire course is packed with practical information, articles, and videos to help you understand the entire process of viral sequencing. This course is part of a series of courses developed by COVID-19 Genomics Global Training or COG-Train. An initiative to develop SARS-CoV-2 genomics capacity worldwide. We hope you enjoy the course and the discussions with colleagues from all around the world.


  • Week 1

    Fundamentals of viral sequencing

    • Welcome to Week 1

      Here we will introduce you to the Educators and contributors of this course and provide helpful information about the course.

    • Introduction to viral genomics and sequencing

      Review basic concepts of the SARS-CoV-2 genome and sequencing technologies

    • Sequencing approches for SARS-CoV-2

      Learn about the main sequencing platforms used the sequence SARS-CoV-2 genomes

    • Ensuring sample and data quality

      Discover how to collect and store samples for high-quality sequencing data

    • End of Week 1

      Review what you have learned this week and assess your progress

  • Week 2

    Library preparation and sequencing

    • Protocols for SARS-CoV-2 whole-genome sequencing

      Discuss the pros and cons of the most commonly used protocols for SARS-CoV-2 sequencing

    • Fundamentals of library preparation and sequencing

      Learn the details of the main methodologies used for library preparation and sequencing

    • Practical considerations for scaling up

      How do you go from sequencing one sample to sequencing thousands of them? Learn tips and tricks from the experts

    • End of Week 2

      Check how your learning progress is going

  • Week 3

    Sequencing analyses and interpretation

    • Data quality control

      Learn how to access data and assess its quality

    • Basic analyses for SARS-CoV-2

      Introduction of viral genetic diversity analyses

    • How to share your data with the world

      An overview of consent, public health reports and how to establish international collaborations

    • End of Week 3

      Check what you have learnt in this course and discover what is next

Learning on this course

On every step of the course you can meet other learners, share your ideas and join in with active discussions in the comments.

What will you achieve?

By the end of the course, you‘ll be able to...

  • Compare sequencing methodologies
  • Critically evaluate different approaches to determine SARS-CoV-2 genomes and variants
  • Apply SARS-CoV-2 sequencing best practices
  • Identify ways in which to scale up SARS-CoV-2 sequencing
  • Describe SARS-CoV-2 analysis pipelines

Who is the course for?

This course is designed for diagnostic and healthcare professionals, researchers, and anyone involved in the testing and analysis of COVID-19 samples.

What software or tools do you need?

No formal prerequisites. Basic knowledge of molecular biology techniques and DNA sequencing methodologies will be advantageous.

Who will you learn with?

I use nanopore sequencing to discover novel, plastic-degrading enzymes in the environment.

Molecular microbiologist | University of Portsmouth | COG-UK Key Contributor | @angelabeckett10

I am an Applications Specialist at UCL Genomics, performing NGS and specialising in WGS of pathogens by target enrichment, usually in a high-throughput way.

Working as Associate Professor at Central Research Laboratory, KIMS, Bengaluru. PhD graduate with 17yrs of research experience in Genomics, Molecular biology, microbiology, proteomics and immunology.

I am a professor of microbiology at Universidad Peruana Cayetano Heredia and a visiting research scholar at the Wellcome Sanger Institute. I study how pathogen populations evolve and spread in Peru.

I am the Head of Sequencing at UCL Genomics. The facility sequenced SARS-CoV-2 samples for COG-UK and also specialises in pathogen WGS directly from clinical samples using targeted enrichment.

Who developed the course?

Wellcome Connecting Science

Wellcome Connecting Science develops and delivers open postgraduates courses and conferences focused on biomedicine.


COG-Train is an educational initiative developed jointly by the COVID-19 Genomics UK (COG-UK) consortium and Wellcome Connecting Science (WCS) to provide open-access learning in SARS-CoV-2 genomics.

What's included?

Wellcome Connecting Science are offering everyone who joins this course a free digital upgrade, so that you can experience the full benefits of studying online for free. This means that you get:

  • Unlimited access to this course
  • Includes any articles, videos, peer reviews and quizzes
  • Tests to validate your learning
  • A PDF Certificate of Achievement to prove your success when you’re eligible
  • Learning on FutureLearn

    Your learning, your rules

    • Courses are split into weeks, activities, and steps to help you keep track of your learning
    • Learn through a mix of bite-sized videos, long- and short-form articles, audio, and practical activities
    • Stay motivated by using the Progress page to keep track of your step completion and assessment scores

    Join a global classroom

    • Experience the power of social learning, and get inspired by an international network of learners
    • Share ideas with your peers and course educators on every step of the course
    • Join the conversation by reading, @ing, liking, bookmarking, and replying to comments from others

    Map your progress

    • As you work through the course, use notifications and the Progress page to guide your learning
    • Whenever you’re ready, mark each step as complete, you’re in control
    • Complete 90% of course steps and all of the assessments to earn your certificate

    Want to know more about learning on FutureLearn? Using FutureLearn

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