Animal Genome Informatics
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Date:
Monday 29 September - Friday 3 October 2014Venue:
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication deadline:
Friday 15 August 2014Participation:
Open application with selectionContact:
Frank O’DonnellRegistration fee:
£400Registration closed
Overview
This course will provide an overview of key issues in animal informatics, bioinformatics tools, and procedures for the analysis and annotation of the genomes sequences of animals, with an emphasis on the analysis of NGS data. It will be delivered using a mixture of lectures, computer-based practical sessions and interactive discussions. The course will provide a platform for discussion of the key questions and challenges in the field.
Audience
The course is aimed at researchers with some experience of working on animal genome data, and who want to become more proficient in large scale data analysis. Applicants should have familiarity with unix/R and using the command line, or must learn these skills prior to attending the course. Free tutorials are available at the following URLs:
Syllabus, tools and resources
During this course you will learn about:
- NGS: QC, read mapping, variant calling, DNA assembly, SNP genotyping
- Annotation: SNP and gene annotation
- Public repositories: Ensembl
Outcomes
After this course you should be able to:
- Use public repositories to search, browse and obtain genomic data
- Describe and implement a range of techniques to analyse NGS data
- Evaluate the advantages and disadvantages of methods to annotate livestock genomes
- Discuss major challenges in the field
Programme
| Time | Topic | Trainer |
|---|---|---|
| Day 1 - Monday 29 September - Introduction to course and to NGS | ||
| 10:00 - 10:30 | Registration and tea/coffee | |
| 10:30 - 11:00 | Welcome and introduction | Laura Emery |
| 11:00 - 12:30 | NGS basic concepts with group activity | Rennan Moreira, Rodrigo Secolin and Samara Kiihl |
| 12:30 - 13:30 | Lunch | |
| 13:30 - 15:00 | Exploring livestock data with Ensembl | Denise Carvalho-Silva |
| 15:00 - 15:30 | Tea/coffee break | |
| 15:30 - 17:00 | Quality control for NGS data including practical | Mitra Barzine |
| 17:00 - 18:00 | Keynote lecture | Alan Archibald |
| 18:00 - 18:30 | Networking activity | |
| 19:00 | Evening meal @ Red Lion pub Hinxton (www.redlionhinxton.co.uk) | |
| Day 2 - Tuesday 30 September - NGS mapping and assembly | ||
| 09:00 - 10:30 | Read mapping with practical | Ian Streeter |
| 10:30 - 11:00 | Tea/coffee break | |
| 11:00 - 12:30 | Read mapping with practical (Cont.) | Ian Streeter |
| 12:30 - 13:30 | Lunch | |
| 13:30 - 14:30 | Advice for DNA assembly | Alan Archibald |
| 14:30 - 15:30 | SNP calling with practical | Ian Streeter |
| 15:30 - 16:00 | Tea/coffee break | |
| 16:00 - 17:30 | SNP calling with practical (Cont.) | Ian Streeter |
| 17:30 - 18:30 | Discussion | All |
| 19:00 | Evening meal @ Wellcome Trust Conference Centre | |
| Day 3 - Wednesday 1 October - NGS variant calling and annotation | ||
| 09:00 - 10:30 | SNP annotation with VEP practical | Will McLaren |
| 10:30 - 11:00 | Tea/coffee break | |
| 11:00 - 12:30 | SNP annotation with VEP practical (Cont.) | Will McLaren |
| 12:30 - 13:30 | Lunch and poster session | |
| 13:30 - 15:00 | RNA-seq applications with group activity | Fabiano Pais and Gabriel Fernandes |
| 15:00 - 15:30 | Tea/coffee break | |
| 15:30 - 17:30 | Using RNA-seq data to inform annotation with practical (Cont.) | Thibaut Hourlier & Konstantinos Billis |
| 17:30 - 18:30 | Discussion | All |
| 19:00 | Evening meal @ Wellcome Trust Conference Centre | |
| Day 4 - Thursday 2 October - Annotating animal genomes | ||
| 09:00 - 10:30 | DNA assembly with practical | Daniel Zerbino |
| 10:30 - 11:00 | Tea/coffee break | |
| 11:00 - 12:30 | DNA assembly with practical (Cont.) | Daniel Zerbino |
| 12:30 - 13:30 | Lunch | |
| 13:30 - 15:00 | Comparative analyses | Marlies Dolezal |
| 15:00 - 15:30 | Tea/coffee break | |
| 15:30 - 17:30 | Comparative analyses (Cont.) | Marlies Dolezal |
| 19:00 | Evening meal @ Wellcome Trust Conference Centre | |
| Day 5 - Friday 3 October - Functional genomics (ChIP-seq analysis) | ||
| 09:00 - 10:30 | ChIP-Seq annotation | Lel Eory |
| 10:30 - 11:00 | Tea/coffee break | |
| 11:00 - 12:30 | ChIP-Seq annotation (Cont.) | Lel Eory |
| 12:30 - 13:00 | Course feedback and wrap up | Laura Emery |
| 13:00 - 13:30 | Lunch | |
| 13:30 | End of course | |
In association with
How to apply
Registration for this course has now closed.
Application deadline
15 August 2014
Number of places
30 places
Organisers
Laura Emery
Trainers
Lel Eory - Roslin Institute, Edinburgh University, UK
Mitra Barzine - EMBL-EBI, UK
Alan Archibald - Roslin Institute, Edinburgh University, UK
Ian Streeter - EMBL-EBI, UK
Marlies Dolezal - University of Veterinary Medicine Vienna, Austria
Konstantinos Billis - EMBL-EBI, UK
Laura Emery - EMBL-EBI, UK
Will McLaren - EMBL-EBI, UK
Daniel Zerbino - EMBL-EBI, UK
Denise Carvalho-Silva - EMBL-EBI, UK
Thibaut Hourlier - EMBL-EBI, UK