Course at EMBL-EBI

Livestock genomics

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This course will introduce participants to methods and approaches for analysing genomic data from common livestock species. It will guide participants through understanding the theory of next generation sequencing methods, and how these are applied in the field of livestock genomics. Over the course participants will learn about resequencing genomes, locating variant data, annotating a genome sequence using transcriptomics data and how to begin ascribing function to genes and genomic regions. The content will also explain how to make use of existing public data, submit and share your discoveries with the community and draw on relevant use cases in the field.

Who is this course for?

This course is aimed at PhD students and postdoctoral researchers needing to learn about methods and approaches for manipulating and analysing livestock genomic data. It will help those wanting to start basic identification of genetic variation, annotating function to genomic data, and using public data to interpret new findings.

Participants will require a basic knowledge of the Unix command line, the Ubuntu 18 operating system and the R statistical packages. We recommend these free tutorials:

Regardless of your current knowledge we encourage successful participants to use these, and other materials, to prepare for attending the course and future work in this area.


What will I learn?

Learning outcomes

During this course you will learn about:

  • Basics of NGS technologies
  • Read mapping, variant calling and GWAS
  • Genebuild/Ensembl Annotation
  • Ensembl Browser + data resources for genomics
  • Relevant genomics use cases in key livestock species
Course content

During this course you will learn about:

  • Basics of NGS technologies
  • Read mapping, variant calling and GWAS
  • Genebuild/Ensembl Annotation
  • Ensembl Browser + data resources for genomics
  • Relevant use cases


Piraveen Gopalasingam
Thibaut Hourlier
Francisco Lobo
Federal University of Minas Gerais (UFMG), Brazil
Cath Brooksbank
Alan Archibald
Roslin Institute, Edinburgh University, UK
Sam Holt
Baron Koylass
Astrid Gall
Juan Pablo Nani
INTA, Argentina
Kostas Billis
Jane Loveland
Silvie Fexova
Wendy Acuna
Instituto Nacional de Innovación Agraria (INIA), Perú
Manuel More
Universidad Nacional Agraria La Molina, Perú
Rafael Penha Filho
Sao Paulo State University (UNESP), Brazil
Diana Lopez
Universidad Nacional de Colombia, Colombia
Natalia Pin Viso
INTA Castelar, Buenos Aires, Argentina


Day 1 – Monday 1 April 2019
10:00-10:30 Arrival, registration and refreshments  
10:30 -11:00 Welcome and introduction to EMBL-EBI Piv Gopalasingam
11:00-12:00 Livestock genomics in Latin America and CABANA’s role in capacity strengthening Cath Brooksbank
12:00-13:00 Introductions, networking and expectations Piv Gopalasingam
13:00-14:00 Lunch and posters  
14:00-15:00 Introduction to genomics CABANA Trainers
15:00-15:30 Break  
15:30-17:00 NGS bioinformatics file formats practical CABANA Trainers
17:00-18:00 Using NGS methods for livestock genomics CABANA Trainers
18:15 Check in to accommodation  
19:30 Evening meal Hinxton Hall Restaurant
Day 2 – Tuesday 2 April 2019
08:45 Arrival  
09:00-10:00 Functional annotation of animal genomes and the importance of reference genomes for livestock research Paul Flicek
10:00-10:30 Break
10:30-12:00 Genomes and manual annotation Jane Loveland
12:00-13:00 Lunch and posters
13:00-15:00 Ensembl genome annotation Thibaut Hourlier & Kostas Billis
15:00-16:00 Introduction to Ensembl Astrid Gall
16:00-16:30 Break  
16:30-18:30 Genes and transcripts and comparative genomics Astrid Gall
19:00 Evening meal Hinxton Hall Restaurant
Day 3 – Wednesday 3 April 2019
08:30 Arrival, registration  
09:00-10:00 Forward and reverse genetics approaches to infectious disease in farmed animals Alan Archibald
10:00-10:30 Break  
10:30-11:30 Genome resequencing Francisco Lobo
11:30-13:00 Resequencing and variant calling practical Francisco Lobo
13:00-14:00 Lunch and posters  
14:00-16:00 Resequencing and variant calling practical Francisco Lobo
16:00-16:30 Break  
16:30-17:30 Resequencing and variant calling practical Francisco Lobo
17:30-18:30 Variation in Ensembl Astrid Gall
18:30 End of day  
19:30 Dinner Hinxton Hall Restaurant
Day 4 – Thursday 4 April 2019
08:45 Arrival  
09:00-10:00 Interpretation of variant effects using VEP Astrid Gall
10:00-11:00 Genome Wide Association Studies Juan Pablo Nani
11:00-11:15 Break  
11:15-12:45 GWAS practical Juan Pablo Nani
12:45-13:15 GWAS data resources Juan Pablo Nani
13:15-14:00 Lunch and posters  
14:00-16:00 Data resources for variant data: EVA Baron Koylass
16:00-16:30 Break  
16:30-18:30 BioMart, Data upload Astrid Gall
18:30 End of day  
19:30 Evening meal Hinxton Hall Restaurant
Day 5 - Friday 5 April 2019
08:30 Check out of accommodation  
08:45 Arrival  
09:00-10:00 Discovering nucelotide sequences with ENA Sam Holt
10:00-10:30 Break  
10:30-11:45 Exploring gene expression data with Expression Atlas Silvie Fexova
11:45-12:15 Course wrap-up and feedback Piv Gopalasingam
12:15-13:00 Lunch  
13:00 Shuttle to Cambridge Station  

Please read our page on application advice before starting your application. In order to be considered for a place on this course, you must do the following:

  1. Complete the online application form
  2. Provide a Microsoft Word (.docx) document containing three short paragraphs with a biography, work history and description of your current research interests; each paragraph should be no more than 100 words
  3. Provide a letter of support from a supervisor or a senior co-worker explaining why you should be selected for this course

Incomplete applications will not be considered.

CABANA Travel Fellowships & Course Fee Bursary

The CABANA project has made available funds to provide 10 successful applicants from Latin American countries with a bursary to cover 100% of the course fee and up to £1125 towards travel costs. If you fulfill the selection criteria and wish to apply for a CABANA Travel Fellowship or Course Fee Bursary please complete this form in addition to your application.

Participants have the opportunity to display an A2 (420x594mm - portrait) poster for the duration of the course. We will ask you to submit your poster before the course for printing on site. It is not possible to display posters of a different size or orientation.

Accommodation will be provided in the Wellcome Genome Campus Conference Centre Monday-Friday inclusive. Please contact the Conference Centre directly if you wish to arrange to stay additional nights. The course fee includes breakfast and evening meals at Hinxton Hall, as well as breaks and lunches outside the EMBL-EBI training rooms.


This course has ended

01 - 05 April 2019
European Bioinformatics Institute United Kingdom
Marina Pujol

  • Tom Hancocks
  • Piraveen Gopalasingam

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