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
Lucas Freitas
Fundação Oswaldo Cruz (Fiocruz)
James Otieno
Fogarty International Center
Pedro E. Romero
Universidad Peruana Cayetano Heredia
Nídia Trovão
Fogarty International Center
Gabriel da Luz Wallau
Fundação Oswaldo Cruz - Instituto Aggeu Magalhães
Nadim Mahdi Rahman
EMBL-EBI
Juan Sebastián Andrade Martínez
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

Applications closed
27 July 2022

17 - 21 October 2022
£200
Contact
Sophie Spencer
Open application with selection
30 places

Organisers
  • Dayane Rodrigues Araujo
    EMBL-EBI
  • Pedro E. Romero
    Universidad Peruana Cayetano Heredia

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