• Wellcome Connecting Science
  • COG Train png logo
New

Making sense of genomic data: COVID-19 web-based bioinformatics

Explore the tools for web-based SARS-CoV-2 sequencing analyses and learn techniques to prepare data and share genomic outputs.

Genetic Research, a closeup of a male scientist viewing DNA information on a wide computer screen screens with blue, red , yellow and green colour representing different data
  • Duration

    3 weeks
  • Weekly study

    5 hours
  • 100% online

    How it works
  • Digital upgrade

    Free

Discover how to analyse SARS-CoV-2 sequences using web-based tools

Over the past decade, sequencing technologies have become more accessible and sequencing data has increased exponentially. However, bioinformatics capacity is still limited.

On this three-week course, you will learn the basics of bioinformatics concepts and explore the web-based tools used for viral data and sequencing analyses.

Develop your understanding of bioinformatics and SARS-CoV-2 data analysis

Although testing and sequencing capacity has improved, in low-and-middle-income countries (LMICs) bioinformatics analyses still represent a bottleneck in the implementation of effective viral surveillance programmes.

This course will introduce you to SARS-CoV-2 bioinformatics pipelines. You will then learn how to use the web-based tool Galaxy for bioinformatics analyses, including how to input and process data, build a pipeline, and use existing workflows.

Explore the process of identifying SARS-CoV-2 variants across global networks

Using COVID-19 as an example, you’ll be introduced to genomic epidemiology through the lens of data sharing across global networks. You will examine best practices for data sharing in public databases.

Then, you will move on to explore phylogenetics, the best tools to use, and the models developed for SARS-CoV-2 analyses. To tie it all together, you will learn how to create and share public health reports.

Learn from global experts in bioinformatics

The educators and developers of this course are experts in bioinformatics working on data analyses and SARS-CoV-2 bioinformatics in different parts of the world. With this experience, the team is uniquely positioned to help you understand and get a step up in web-based SARS-CoV-2 bioinformatics.

Syllabus

  • Week 1

    Introduction to viral genomics

    • Welcome to the course

      An introduction to this course, and advice for maximising your learning.

    • Introduction to viral sequencing

      Introductions to viral sequencing - the way of determining the genetic code of viruses

    • Next-Generation Sequencing data formats

      An introduction to the data formats used in the processing of genetic sequencing

    • Introduction to web-based bioinformatics

      How to start using Galaxy and other web-based tools

    • End of Week 1

      Review and assessment of your learning progress

  • Week 2

    Exploring the pipelines available

    • Quality of data

      An overview of the impact of data quality

    • Data preparation

      A discussion on quality control and tools

    • Predicting lineages and variants

      Learn how to identify SARS-CoV-2 variants and classify it into lineages

    • Phylogenetics and epidemiology

      Discover how to reconstruct a phylogenetic tree and how to apply it in epidemiological approaches

    • End of Week 2

      Assess and reflect your learning progress

  • Week 3

    Introduction to genomic epidemiology of COVID-19

    • Metadata and bioethics

      Learn what is metadata and the ethical concerns to use genomics and clinical data

    • Sharing data in public databases

      Learn more about data sharing and public databases

    • Using and displaying viral genomic data

      Insights on the generation of reports used in public health approaches

    • End of Week 3

      Assess what you have learned in this course and discover the next steps

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.

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...

  • Describe the SARS-CoV-2 viral genomic structure
  • Evaluate different sequence analysis outputs
  • Apply a basic analytical web-based pipeline
  • Investigate how variant calling contributes to epidemiological inferences

Who is the course for?

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

It will also be useful to researchers specialising in web-based bioinformatics, diagnostics, diseases, or pandemics.

What software or tools do you need?

No formal prerequisites. Basic knowledge of analysis tools using Galaxy or UNIX systems will be useful.

Who will you learn with?

I'm a Ph. D. caniddate in the Biomedical Sciences programme at UNAM, Mexico. I work identifying genetic variation (rare and common) that predisposes to develop cancer.

I am a PhD candidate at Wits University and the CSIR in South Africa. I am currently investigating human gut microbiome characterization using bioinformatics analyses of a South African population.

Senior Lecturer in Computational Microbiology at Sydney ID (University of Sydney) and affiliated with the Big Data Institute (University of Oxford).

Tracey Calvert-Joshua is a bioinformatician and a PhD student at the South African National Bioinformatics Institute. She worked in cancer genomics, operon prediction and SARS CoV-2 data analysis.

I am Senior Bioinformatician at Central Research Laboratory, KIMS, Bengaluru

Who developed the course?

Wellcome Connecting Science

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

COG-Train

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

    Do you know someone who'd love this course? Tell them about it...

    You can use the hashtag #CovidBioinformatics to talk about this course on social media.