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
Filipe Zimmer Dezordi
Fundação Oswaldo Cruz - Instituto Aggeu Magalhães James Otieno
Theiagen Genomics Maira Ihsan
EMBL-EBI Pedro E. Romero
Universidad Peruana Cayetano Heredia Nídia Trovão
Fogarty International Center Gabriel da Luz Wallau
Fundação Oswaldo Cruz - Instituto Aggeu Magalhães Zahra Waheed
EMBL-EBI Juan Sebastián Andrade Martínez
Cornell University Michael Quail
Sanger Institute Daniel Vincent Thomas Lopez
EMBL-EBI
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
Zahra Waheed
11:30 – 12:30
Approaches to virus sequencing – Covid et al!
Michael Quail
12:30 – 13:30
Lunch break
13:30 – 14:30
Sequence retrieval
Maira Ihsan
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 learnt 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 learnt 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 learnt 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
09:00 - 12:00
Self-study - try what you've learnt on your own
12:00 - 13:00
Lunch break
13:00 – 14:00
Public health and policy
Daniel Vincent Thomas Lopez
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.
Fundação Oswaldo Cruz - Instituto Aggeu Magalhães
Theiagen Genomics
EMBL-EBI
Universidad Peruana Cayetano Heredia
Fogarty International Center
Fundação Oswaldo Cruz - Instituto Aggeu Magalhães
EMBL-EBI
Cornell University
Sanger Institute
EMBL-EBI
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 |
Zahra Waheed |
|
11:30 – 12:30 |
Approaches to virus sequencing – Covid et al! |
Michael Quail |
|
12:30 – 13:30 |
Lunch break |
|
|
13:30 – 14:30 |
Sequence retrieval |
Maira Ihsan |
|
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 learnt 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 learnt 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 learnt 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 |
||
| 09:00 - 12:00 | Self-study - try what you've learnt on your own | |
| 12:00 - 13:00 | Lunch break | |
|
13:00 – 14:00 |
Public health and policy |
Daniel Vincent Thomas Lopez |
|
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.