Livestock Genomics

Date:

 Monday 1 Friday 5 April 2019

Venue: 

European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus Hinxton,  Cambridge CB10 1SD,  United Kingdom

Application opens: 

Monday 22 October 2018

Application deadline: 

Friday 25 January 2019

Participation: 

Open application with selection

Contact: 

Marina Pujol

Registration fee: 

£300

Overview

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.

Audience

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.

We strongly endorse applications from Latin American students who will be able to benefit from the CABANA funding available as part of this course.

Syllabus, tools and resources

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
     

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

Additional information

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.

Accommodated 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 Sunday-Monday. The course includes breakfast and evening meals at Hinxton Hall, and breaks and lunches outside the EMBL-EBI training rooms.

CABANA Travel Fellowships & Course Fee Bursary

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.

Programme

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 Introductions, networking and expectations All, led by CABANA partners
12:00 - 12:30 Livestock genomics in Latin America and CABANA’s role in capacity strengthening Cath Brooksbank
12:30 - 13:30 Lunch and posters  
13:30 - 14:30 Introduction to genomics CABANA partners
14:30 - 15:30 Using NGS methods for livestock genomics To be confirmed
15:30 - 16:00 Break  
16:00 - 17:30 NGS bioinformatics file formats practical CABANA partners
17:30 - 18:30 Forward and reverse genetics approaches to infectious disease in farmed animals Alan Archibald
18:45 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 annotation Jane Loveland
12:00 - 13:00 Lunch and posters
13:00 - 15:00 Ensembl Genebuild Thibaut Hourlier
15:00 - 16:00 Browsing genomes with Ensembl Ensembl Outreach
16:00 - 16:30 Break  
16:30 - 18:30 Browsing genomes with Ensembl Ensembl Outreach
19:00 Evening meal Hinxton Hall Restaurant

 

Day 3 – Wednesday 3 April 2019
08:30 Arrival, registration  
09:00 - 10:30 Genome resequencing Francisco Lobo
10:30 - 11:00 Break  
11:00 - 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  
16:30-18:30 Interpretation of variant effects Ensembl Outreach
17:30 - 18:30 Data resources for variant data  
19:30 Dinner Hinxton Hall Restaurant
Day 4 – Thursday 4 April 2019
08:45 Arrival  
09:00-11:00 Genome Wide Association Studies To be confirmed
11:00 - 11:30 Break  
11:30-12:30 GWAS practical To be confirmed
12:30 - 13:00 GWAS data resources To be confirmed
13:00 - 14:00 Lunch and posters  
14:00-16:00 Browsing genomes with Ensembl Ensembl Outreach
16:00-16:30 Break  
16:30-18:30 Browsing genomes with Ensembl Ensembl Outreach
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 - 09:45 FAANG, the European Nucleotide Archive, and the importance of good metadata Peter Harrison
09:45 - 10:45 Discovering nucelotide sequences with ENA Sam Holt
10:45-11:15 Break  
11:15-12:15 Feedback and wrap-up Piv Gopalasingam
12:15 - 13:00 Lunch  
13:00 Coach to Cambridge railway station  

Modules

  • ensemblensembl-genomes
  • european-nucleotide-sequence-archive-ena
  • european-variation-archive-eva