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From Swab to Server: Testing, Sequencing, and Sharing During a Pandemic

Discover the process of how swab samples become critical data that aid the knowledge and understanding of the spread of disease.

3,416 enrolled on this course

A person holding a sample tube labelled as COVID-19 test negative
  • Duration

    3 weeks
  • Weekly study

    5 hours
  • 100% online

    How it works
  • Digital upgrade


Explore the journey from swabbing to processing data

Sampling and testing are key to understanding where a disease is spreading. In the COVID-19 pandemic, the number of samples taken, analysed, tracked, and shared have far surpassed any previous pandemic.

On this three-week course from COG-Train, you will learn about the process that samples undergo to become datasets. You’ll also gain the knowledge of how this data is handled in order to satisfy public health concerns during a pandemic.

Discover how sample strategies can affect scientific research and results

Sampling is a critical part of research in any field. In studying a disease such as Covid-19, it’s imperative that your sample and sampling methods are best-suited to reflect accurate results.

Supported by expert educators, you will explore different sample methods to examine their efficacy. With this knowledge, you’ll be equipped to discuss sampling strategies and their correct applications.

Delve into the ethics of data sharing on a pandemic scale

Data from samples provides scientists with the essential information they need to analyse and track a disease.

However, this sample data can contain highly personal information about the population. You’ll discuss the ethical implications of using and sharing data and consider methods of protecting personal information.

Recognise the importance of data sharing and linkage in public health concerns

Linking genomic data sets to clinical and epidemiological data sets can help us understand the effects of different variants, which is especially prevalent for Covid-19.

With the help of COG-Train, you’ll learn to create holistic datasets through linkage. With this knowledge, you’ll further your understanding of Covid-19 and use your findings to address concerns related to public health.

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Skip to 0 minutes and 17 seconds Welcome to the course “From Swab to Server: Testing, Sequencing, and Sharing During a Pandemic.” In this course, you will learn the journey of a COVID-19 sample from its collection through the generation of sequencing and clinical data, then share the data with partners and the world. You may have an experience in testing and analysis of the clinical samples or an interest in diagnostics on pandemic skills, or even just be here to learn more. This course will give you an overview of how experts around the world have overcome the challenges of large-scale testing, sequencing, and data-sharing during the pandemic. In week one, you will be introduced to the testing and data generation workflow.

Skip to 1 minute and 7 seconds You will learn about the different sample types and the measures that should be taken to obtain reliable results. You will hear experts discussing the challenges faced during the pandemic, how they implemented reliable and integrated testing facilities. We will also cover the lessons learned on high throughput data generation and how they avoided the major pitfalls of this process. In week two, we will go deeper into the data associated with the clinical samples, or metadata. You will understand the benefits of biobanking and learn good practises for data collection. We will also discuss how to collect and enrich metadata and what is necessary to keep the data robust and secure.

Skip to 1 minute and 54 seconds By the end of the second week, you would have learned from defined professionals the role of metadata on surveillance and epidemiology and research. In week three, you will learn the ethical implications of data sharing. We will talk about the principles and best practices for sharing data with stakeholders across the globe. We will hear from global experts how they exchange information during the pandemic and what the benefits and challenges are. We hope you enjoy the course.


  • Week 1

    The journey of a sample

    • Welcome to week 1

      Introduction to the course series and what is coming on the next three weeks

    • Sample to server

      Learn about the different types of samples and SARS-CoV-2 testing

    • Sampling strategy

      The different sources of samples and how to sample efficiently

    • Implementation of testing and sequencing

      How to implement and scale-up testing and sequencing during a pandemic

    • End of Week 1

      Test and share what you have learned so far

  • Week 2

    How to make data richer

    • Welcome to Week 2

      Welcome back! This week you will learn about biobanking and meta-data

    • Metadata

      What meta-data is and how to generate it.

    • Data enrichment

      Learn how to make your data more beneficial

    • Data integration

      The challenges and technical requirements to integrate sample and data

    • End of Week 2

      Review, test and share what you have learned.

  • Week 3

    A sample without data is nothing

    • Welcome to Week 3

      How to be prepared and share data during and between public health emergencies

    • How to share different types of data

      Discover how public health data has been shared in the world

    • Data sharing

      Learn about the best practices to share data with collaborators and in public databases

    • Sharing FAIR-ly

      Overview of how to promote international collaboration and data sharing

    • End of Week 3

      Test what you have learned and stay tuned about our next courses

When would you like to start?

Start straight away and join a global classroom of learners. If the course hasn’t started yet you’ll see the future date listed below.

  • Available now

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...

  • Outline the journey from sample collection, through PCR to sequencing and data linkage
  • Compare the different sample types and how sampling strategy affects test performance
  • Explain the importance of linking genomic data to clinical and epidemiological data sets to address public health and scientific questions
  • Identify and explore ethical, legal and social implications of data use and sharing

Who is the course for?

This course is designed for diagnostic and healthcare professionals, as well as anyone involved in the testing and analysis of disease samples.

It will also be advantageous to researchers specialising in the fields of pandemics, diseases, and diagnostics.

Who will you learn with?

I work at the MRC-University of Glasgow Centre for Virus Research (CVR), where I oversee the viral genomics team. We provide expertise on high-throughput sequencing applied to viruses.

I am a lecturer in Genomic Medicine at the University of Exeter where I work on genotyping chip accuracy and rare cancer variant penetrance as well as being Scientific Lead for COG-Train

I work with Makerere University as a Coordinator of the Integrated Biorepository of H3Africa Uganda and a Teaching Assistant for Molecular Biology and Human genetics

Biomedical Scientist at the Makerere University Biomedical Research Centre, Uganda. Interested in EvoDevo. My goal in life is to gain a better understanding of the human body.

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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