These materials were part of the live ‘Livestock genomics’ 2024 course. Please refer to the course page to check details about the live event and the original programme.

The content table below outlines the different sessions that were included in the course, as well as the format of the materials (slides/videos/practicals) and each session’s trainer. Either proceed in order through the materials using the arrows at the end of each page, or pick your topic of interest from the table below to skip straight to it.

Before proceeding to carry out some of the course tutorials, we encourage you to revise the Software installed for the practicals page.

 Presentation slides –  View or download the slides

 Recorded lectures – Watch the lecture videos 

 Practicals – View or download the slides, exercises, datasets, analysis scripts and results

Format	Subject	Trainers
	Services and initiatives on livestock genomics
	Introduction to EMBL-EBI: livestock genomics services and ELIXIR animal agriculture efforts	Peter Harrison
	Introduction to Ensembl tools for studying the impact of genomics for precision breeding	Aleena Mushtaq
	FAANG data coordination centre	Alexey Sokolov
	Overview of the BovReg project and using FAANG assays	Gabriel Costa
	From FAANG to fork: highly annotated genomes as resources to improve farmed animal production	Emily Clark
	Pangenomics	Fergal Martin
	Nucleotide discovery and Sequencing techniques
	Discovering nucleotide sequences with the European Nucleotide Archive (ENA)	Maira Ihsan
	Sequencing methods for livestock genomics	Diana Lopez and Juan Diego Duque
	Annotation and comparative genomics
	Ensembl genome annotation	Jose Maria Gonzalez Perez-Silva
	Genomes and manual annotation	Zoe Hollis
	Ensembl genes and transcripts annotation	Aleena Mushtaq
	Comparative genomics	Aleena Mushtaq
	Ensembl regulatory annotation	Gabriela Merino and Paulo Lins
	Extracting and uploading data in Ensembl through the web interface	Aleena Mushtaq
	Gene expression	Silvie Fexova
	Genome Wide Association Studies (GWAS)	Juan Pablo Nani
	Genome resequencing and variant studies
	Variation in Ensembl, Interpretation of variant effects using Ensembl Variant Effect Predictor (VEP)	Aleena Mushtaq
	Genome resequencing and variant calling	Francisco Lobo
	The European Variation Archive (EVA)	Dona Shaju and Tim Cezard
	Good data management	Daniel Thomas Lopez