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.
Duration
3 weeksWeekly study
5 hoursDigital upgrade
Free
Making sense of genomic data: COVID-19 web-based bioinformatics
Other courses you might like
This course isn't running right now. We can email you when it starts again, or check out these other courses you might like.
Browse more in Healthcare & Medicine and Science, Engineering & Maths
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
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:
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
Learner reviews
Learner reviews cannot be loaded due to your cookie settings. Please and refresh the page to view this content.
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.