This hands-on virtual course will introduce participants to methods and approaches for analysing genomic data from common livestock species, including cattle, pig, chicken, and sheep. During the course participants will learn about the use of sequencing methods in the field of livestock genomics, resequencing genomes, locating variant data, annotating genomes, and carrying out GWAS approaches. The course will also cover the use of public EMBL-EBI resources such as Ensembl, EVA, and ENA to progress in your research, as well as to submit and share your discoveries with the community, and will present relevant use cases in the field. The course will enable you to harness the wealth of publicly available farmed animal datasets held in EMBL-EBI public archives and utilise our free services and tools to for example, identify genetic variants associated with disease, identify genetic markers associated with desirable breeding traits, or use Ensembl Variant Effect Predictor (VEP) tool to predict the functional impact of genetic variants. EMBL-EBI is committed to support the livestock research community and industry to improve animal health and welfare, increase productivity, and reduce environmental impact.

Virtual course

Participants will learn via a mix of pre-recorded lectures, live presentations, and trainer-led computational exercises. Live sessions will be delivered using Zoom with additional support and asynchronous communication via Slack.

Pre-recorded material may be provided before the course starts that participants will need to watch, read, or work through to gain the most out of the actual training event. In the week before the course, there will be a brief induction session. Computational practicals will run on EMBL-EBI's virtual training infrastructure, meaning participants will not require access to a powerful computer or install complex software on their own machines.

Participants will need to be available during the course hours, maximum 09:00 – 18:30 GMT each day of the course. Trainers will be available to assist, answer questions, and provide further explanations during these times.

Who is this course for?

This course is mainly 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 utilise the wealth of publicly available data to explore the connection between genotype and phenotype, identify and select traits of interest for precision breeding, identify genetic variants associated with disease and resistance, and gain insight into the latest developments in genomics and pangenomics.

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

• The Unix Shell: https://swcarpentry.github.io/shell-novice/ 
• Basic R concept tutorials: www.r-tutor.com/r-introduction

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

After the course you should be able to: 

• Describe sequencing technologies applicable to livestock genomics
• Carry out mapping, variant calling, and GWAS with genomes of common farmed animals
• Use Ensembl methods and data resources for for studying the impact of genetic variants, genetic diversity, and genomics for precision breeding
• Describe relevant initiatives in the field of livestock genomics

Course content

During this course you will learn about: 

• Sequencing methods
• Annotation of genomes
• Read mapping, variant calling, and GWAS
• Applications of pangenomics and Single Cell Expression Atlas
• Existing initiatives and resources in the field of livestock genomics

Trainers

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

• Complete the online application form.
• Ensure you add relevant information to the ‘submission details’ section where you are asked to provide information on your:
  • pre-requisite skills and knowledge
  • current work and course expectations
  • data availability
• Upload one letter of support from your supervisor or a senior colleague detailing reasons why you should be selected for the course.

Please submit all documents during the application process by 23:59 on 3 December 2023. Items marked * in the application are mandatory. Incomplete registrations will not be processed. 

All applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by 18 December 2023. If you have any questions regarding the application process please contact Sophie Spencer.

The registration fee of £100.00 includes a bespoke course handbook with links to all course materials

Posters

All participants are expected to present a poster during a virtual poster session. Successful applicants will be asked to submit their poster upon registration. 

All posters should:

•          be in a portrait orientation
•          include your photograph and contact information

We expect the posters to act as a talking point between you, other participants and the trainers on the course. They should give the reader an idea of the work you are engaged in, what you are planning to do next, and anything of interest that might be useful for sharing with the gathered participants.