Virtual course
Bioinformatics approaches to viruses
This workshop will provide training on the use of bioinformatics tools to understand viral pathogens’ sequencing data. Trainees will receive training on viral genome assembly, comparative viral genomics, phylogenomics, metaviromics, and downstream applications of this data in research and applied contexts.
Who is this course for?
This course is suitable for postgraduate (MSc-level and above) scientists who are working with or generating genomic datasets related to communicable diseases. Ideally, trainees will be working in the field of virology. We welcome applications from universities, research centres, hospitals, public health, and private laboratories.
What will I learn?
Learning outcomes
After the course you should be able to:
- Establish best analysis practices
- Know the main public repositories for virus sequences
- Analyse and compare genomic sequences of viruses
- Use analytical and visualisation tools for epidemiological understanding and outbreak response
Course content
During this course you will learn about:
- Viral genome databases and sequence retrieval
- Comparative analysis of viral genomes
- Phylogenetics and transmission analysis
Trainers
Fundação Oswaldo Cruz - Instituto Aggeu Magalhães
Fundação Oswaldo Cruz (Fiocruz)
Fogarty International Center
Universidad Peruana Cayetano Heredia
Fogarty International Center
Fundação Oswaldo Cruz - Instituto Aggeu Magalhães
EMBL-EBI
Cornell University
Programme
All timings are in BST.
|
Time |
Topic |
Trainer |
|
Day one – Monday 17 October 2022 |
||
|
09:00 – 10:00 |
Welcome and introductions |
Dayane Araújo |
|
10:00 – 10:30 |
Break |
|
|
10:30 – 11:30 |
EMBL-EBI COVID-19 data portal |
Nadim Rahman |
|
11:30 – 12:30 |
Sequencing technologies |
|
|
12:30 – 13:30 |
Lunch break |
|
|
13:30 – 14:30 |
Sequence retrieval |
Lucas Freitas |
|
14:30 – 15:00 |
Break |
|
|
15:00 – 16:00 |
Sequence quality control |
Gabriel Wallau and Filipe Dezordi |
|
16:00 – 17:00 |
Networking |
|
|
17:00 |
End of day |
|
|
Time |
Topic |
Trainer |
|
Day two – Tuesday 18 October 2022 |
||
|
09:00 – 12:00 |
Self-study - try what you’ve learned on your own |
|
|
12:00 – 13:00 |
Lunch break |
|
|
13:00 – 14:30 |
Assembly of viral genome |
Gabriel Wallau and Filipe Dezordi |
|
14:30 – 15:00 |
Break |
|
|
15:00 – 17:00 |
Comparative analysis of viral genomes |
Gabriel Wallau and Filipe Dezordi |
|
17:00 |
End of day |
|
|
Time |
Topic |
Trainer |
|
Day three – Wednesday 19 October 2022 |
||
|
09:00 – 12:00 |
Self-study - try what you’ve learned on your own |
|
|
12:00 – 13:00 |
Lunch break |
|
|
13:00 – 14:00 |
Introduction to phylogenomics methods |
Nídia Trovão |
|
14:00 – 14:30 |
Break |
|
|
14:30 – 17:00 |
Practical on phylogenomics methods - discrete phylogeography |
James Otieno |
|
17:00 |
End of day |
|
|
Time |
Topic |
Trainer |
|
Day four – Thursday 20 October 2022 |
||
|
09:00 – 12:00 |
Self-study - try what you’ve learned on your own |
|
|
12:00 – 13:00 |
Lunch break |
|
|
13:00 – 14:00 |
Nextstrain resource |
Pedro Romero |
|
14:00 – 14:30 |
Break |
|
|
14:30 – 16:00 |
Metaviromics |
Juan Sebastian Andrade Martinez |
|
16:00 – 17:00 |
Networking |
|
|
17:00 |
End of day |
|
|
Time |
Topic |
Trainer |
|
Day five – Friday 21 October 2022 |
||
|
13:00 – 14:00 |
Public health and policy |
TBA |
|
14:00 – 14:30 |
Break |
|
|
14:30 – 15:30 |
Final discussion |
All trainers |
|
15:30 |
End of course |
|
Please read our page on application support before starting your application. In order to be considered for a place on this course, you must do the following:
- Complete the online application form.
- Ensure you add relevant information to the ‘submission details’ section where you are asked to provide information on your:
- pre-requisite skills and knowledge
- current work and course expectations
- data availability
- Upload one letter of support from your supervisor or a senior colleague detailing reasons why you should be selected for the course.
Please submit all documents during the application process by midnight on 27 July 2022. Items marked * in the application are mandatory. Incomplete registrations will not be processed.
All applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by 10 August 2022. If you have any questions regarding the application process please contact Sophie Spencer.