EMBL-EBI
CABANA Workshop: Plant bioinformatics - analysis of crop genomics data
Date: 13 - 17 December 2021
This course will introduce crop biologists to methods and approaches for analysing crop genomics data for genotyping. During the course participants will learn about genotyping experimental design, variant calling, comparative genomics using Ensembl, analyse variation data with Ensembl Variant Effect Predictor and explore concepts of genome wide association studies (GWAS). The content will explain how to make use of existing public data, retrieve, submit and share your data with the community.
Trainers will cover the basics of diversity analysis using R, before analyzing various genomes to assess diversity, investigating gene-phenotype relationships and microsatellites. The course will be delivered through a combination of hands-on training sessions and lectures.
This course will be a virtual event. The content will be delivered over Zoom. In order to make the most out of the course, you should make sure to have a stable internet connection throughout the week.
Computational practicals will be run on EMBL-EBI's virtual training infrastructure; this means there is no need to have a powerful computer to run exercises or a requirement to install complex software before the course.
Venue: University of Costa Rica (UCR) Ciudad universitaria Rodrigo Facio Brenes
Region: San Jose
Country: Costa Rica
Target audience: This course is aimed at wet-lab researchers within Latin America (excluding Chile and Uruguay due to funding restrictions) who are working with and/or generating their own crop genomic data or who are working on genotyping technologies, including data analysis software development. Researchers who apply for CABANA courses should have projects in one or more of the CABANA challenge areas (sustainable crop production, communicable diseases, protection of biodiversity). Please note this course will be taught in English, however some trainers are fluent in either Spanish/Portuguese, and can offer language support where feasible. Priority will also be given to those who have not attended a CABANA event yet. Scientists from underrepresented ethnic and gender groups are especially encouraged to apply for this workshop, for example women and those with Black and/or Indigenous heritage. Prerequisites: basic computational or previous bioinformatics experience is required for this workshop, such as basic commands in R. Undergraduate-level knowledge of plant biology would be an advantage. Please note: The course will use genomic data from crop plant species throughout the week. It will not explore in detail methods for assembling genomes.
Capacity: 30
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