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.

Who is this course for?

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.

Prerequisites

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:

• Basic introduction to the Unix environment: www.ee.surrey.ac.uk/Teaching/Unix
• Introduction and exercises for Linux: https://training.linuxfoundation.org/free-linux-training

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

What will I learn?

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

Course content

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

Trainers

In order to be considered for a place in this workshop applicants must complete the online application form.

Incomplete applications will NOT be considered.

If you have any queries about the application process please email Guilherme Oliveira and Piv Gopalasingam.

Please note there is NO registration fee and you will not be asked to pay for this workshop.

There will be a maximum of 30 trainees on this workshop and registration is dependent on selection after successful completion of the application process.

Applications will close on Monday 16th November 2020 at 18:30 (COT).

Notification emails will be sent approximately 1 week after the application deadline.