Sequencing viral genomes: hands-on in Costa Rica

Participants of the computational workshop that took place at the Microbiology Faculty at Universidad de Costa Rica

 

Between February 24th - March 4th 2020 the University of Costa Rica hosted the CABANA workshop, “NGS analysis applied to virome sequencing in agricultural systems”.

This workshop was unique in that the first week was focused on nucleic acids extraction (small and large RNAs) and library preparation to sequence on the NextSeq Illumina instrument. For this we had a great team of trainers, Segundo Fuentes and Ana Pérez from CIP; Ivannia Atmetlla, Ricardo Chinchilla and Rebeca Campos from UCR. We wanted a small group (10) of trainees to use the protocols and evaluate whether this wet-lab training could improve their experimental design and understanding of data analysis later on. Though we had some drawbacks, as is natural from wet-lab trainings, some comments from the trainees show the importance of complementing, when possible, bioinformatics training and wet-lab experience:

“The trainers have a lot of experience in the topics covered during the course and they were able to clear all the doubts that emerged during the course of the workshop. It was very useful that one can participate in each step of the library preparation, because I consider that is the only way to really learn the protocol.”

“Everything was good. I learned new techniques, also some procedures I did before but not for NGS so I learned how to adapt it for NGS.”

“The hands-on part. I have the feeling that everyone learns better from doing experiments.

“After the workshop I have been thinking about some ideas for future projects using the knowledge aquired from the course”

“Great experience with well-known trainers and collaborators. I would definitely love to repeat this experience. Thanks CABANA and UCR”

The following week we had a full room (21) of participants from Argentina, Brasil, Colombia, Ecuador, Mexico, Peru, and Costa Rica, to learn the basic analysis to identify and reconstruct viral genomes from small RNAs using the software VirusDetectW, Geneious, RDP and R libraries for network analysis. The trainers Jan Kreuze, Ricardo Alcala and Segundo Fuentes did a great job.

Thank you to all the organizers, trainers and trainees for making this another successful CABANA workshop!