CABANA Workshop: NGS analysis applied to virome sequencing in agricultural systems


 Monday 2 Wednesday 4 March 2020


University of Costa Rica (UCR) - Ciudad universitaria Rodrigo Facio Brenes, San Pedro, San Jose, Costa Rica

Application opens: 

Thursday 05 December 2019

Application deadline: 

Friday 10 January 2020


Open application with selection


CABANA UCR Costa Rica, Rebeca Campos-Sanchez, Jan Kreuze

Registration fee: 

$30000 CRC

Course Overview

This workshop will provide training around the experimental design and multiple applications of Virome Sequencing in agricultural systems. In addition, detailed computational analysis of virome data and resources will be explored. Genomic analysis tools for virome data, such as Virus-DetectW, Phylogenetic and recombination analysis with MegaX and RDP, network analysis using R, as well as publicly available resources for virus analysis and applications will we implemented during the workshop. 

The detection of pathogens is an essential labor for people working on agricultural systems. In recent years the use of sequencing technologies has enabled the discovery and description of new viruses, even communities of pathogenic entities within crops, for example potato and sweet potato. This is relevant for surveillance and to develop strategies to control these pathogens across borders. 

Virome sequencing is a high throughput method to identify and classify communities of viruses, not only in plants but also animals and humans. It relies on viral databases that are constantly evolving. Software is continually being developed as well. Therefore we will explore all of these aspects in this workshop.

Please note: This course is currently under development and full details about the course are not yet available.  Once the programme is confirmed we will post it here along with details on how to apply and registration costs. If you would like to be informed when applications open for this course then please click on the “Register your interest” button above.


This course is aimed mainly at wet-lab researchers at any career stage within Latin America undertaking pathogen population genetics and surveillance, interested in applying next generation sequencing to virus identification. Those working in plant protection organizations and/or academia are welcome to apply, and priority will be given to those who have not yet attended a CABANA workshop.

Knowledge in UNIX and NGS technologies is required. Therefore, these free resources should be studied beforehand: 

Please note this course will be taught in English, however the trainers are fluent in Spanish, and can offer language support where feasible. 
A number of travel fellowships are available for this course - early-stage researchers and researchers from underrepresented groups are especially encouraged to apply for CABANA travel fellowships. You can apply for travel fellowships via the course application form. Priority will be given to those who have not previously been awarded a CABANA fellowship.

Learning outcomes

After this course you will be able to:

  • Plan and design experiments for virome sequencing in your organism of interest
  • Assess applications of virome sequencing to agricultural diseases, biological control
  • Implement pipelines for analyzing viromes and interpretation of results
  • Use public databases for viral genomics


A full programme will be provided shortly.