CABANA Workshop: Applied bioinformatics, molecular epidemiology, and the SARS-CoV-2 Pandemic


 Tuesday 1 Friday 4 December 2020


Virtual - EMBL-EBI, Hinxton,  CB10 1SD, United Kingdom

Application opens: 

Thursday 15 October 2020

Application deadline: 

Monday 16 November 2020


Open application with selection


Piraveen Gopalasingam, Marina Pujol, Marco Cristancho, Diego Forero

Registration fee: 


Registration closed

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Dates additional information: 

This workshop will take place between Tuesday 1st - Friday 4th December, each day running for up to 3 hours.

Course Overview

This workshop will provide training on the use of bioinformatic tools for the design and analysis of research and diagnostic molecular assays. Trainees will receive training on viral genome assembly, comparative viral genomics and downstream applications of this data in research and applied contexts. Trainers will focus practical sessions on the analysis of Illumina SARS-CoV-2 sequences.

This online workshop will be delivered on Zoom and comprise a blend of live lectures and hands-on practicals delivered by trainers across Latin America. Certificates will be provided to mark successful completion of this workshop. Sessions on Friday 4th December will be livestreamed on YouTube and made freely available on the platform thereafter. There will be an opportunity to deliver a short presentation about your work to other trainees.



During this course you will learn about: 

  • Viral genome assembly
  • Comparative analysis of viral genomes
  • Primer design for qPCR
  • Point of care molecular testing
  • Standards for reporting of molecular epidemiology studies



This course is suitable for postgraduate (MSc-level and above) scientists within Latin America (excluding Chile and Uruguay) who are working with or generating genomic datasets related to SARS-CoV-2. Ideally, trainees will be working in the field of virology, and performing sequencing and/or analysing viral sequences, especially those within the coronaviridae family. We welcome applications from universities, research centres, hospitals, public health, and private laboratories.

Scientists from underrepresented ethnic and gender groups are especially encouraged to apply for this workshop.

Please note this course will be taught in English, however the trainers are fluent in either Spanish or Portuguese and can offer language support where feasible. Attendance priority will be given to those who have not attended a CABANA event yet.



Undergraduate-level knowledge of biology would be advantageous. You will also require access to a computer for the duration of the workshop. While most practicals are browser-based, a few will require a UNIX environment. Trainees will therefore require a basic knowledge of the Unix command line.

We recommend these free tutorials:

Training will be delivered via Zoom; trainees need to ensure they have working audio and microphones.

Learning outcomes

After this course you should be able to:

  • Know the main public repositories for virus sequences
  • Analyse genomic sequences of viruses
  • Design PCR primers following international recommendations
  • Apply international standards for the reporting of molecular epidemiology studies


Day 1 – Tuesday 1 December 2020
08:45-09:00 Welcome and introductions Marco Cristancho & Diego Forero
09:00-09:45 Sequencing technologies (Theoretical) Dario Fernandez
09:45-10:30 Viral genomes databases – GISAID and other repositories Priscila Born
10:30-10:45 Break  
10:45-11:30 DNA sequence Quality Control (Theoretical - Practical) Gisele Nunes & Gilderlanio Araujo
11:30-12:00 Trainee presentations Trainees
12:00 End of day 1  
Day 2 – Wednesday 2 December 2020
09:00-11:00 Assembly of viral genomes (Theoretical - Practical)  Jan Kreuze & Segundo Fuentes
11:00-11:15 Break
11:15-12:00 Trainee presentations Trainees
12:00 End of day 2  
Day 3 – Thursday 3 December 2020
09:00-10:00 Comparative analysis of viral genomes (Theoretical - Practical) Dario Fernandez
10:00-11:00 Phylogenomics of viral genomes (Theoretical - Practical)  Dario Fernandez
11:00-11:15 Break
11:15-11:45 Trainee presentations Trainees
11:45 End of day 3  
Day 4 – Friday 4 December 2020
08:45-09:30 Primer design for qPCR (Theoretical)  Segundo Fuentes & Ana Perez
09:30-10:15 Point of care molecular testing (Point of care isothermal amplification protocols) - LAMP (Theoretical)   Segundo Fuentes - Ana Perez 
10:15-10:30 Break
10:30-11:15 Standards for reporting of molecular epidemiology studies - STROBE-ME (Theoretical)  Valentina Gallo
11:15-11:45 Trainee presentations Trainees
11:45-12:00 End of workshop: feedback and certificates Marco Cristancho & Diego Forero


Additional information:

This workshop is part supported by the ITV-Fiocruz coronavirus genome initiative.