Animal Genome Informatics
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
Learning Objectives
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
| 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 | An introduction to NGS for animal informatics, file formats and workflows activity | BPA Trainers |
| 12:30 - 13:30 | Lunch | |
| 13:30 - 15:00 | Exploring livestock data with Ensembl | Ensembl Outreach Team |
| 15:00 - 15:30 | Tea/coffee break | |
| 15:30 - 17:00 | Quality control for NGS data including practical | Mitra Barzine (TBC) |
| 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) | |
| 20:30 | Transport to Holiday Inn, Whittlesford | |
| Day 2 - Tuesday 30 September - NGS mapping and assembly | ||
| 08:30 | Transport from Holiday Inn to campus | |
| 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 @ Red Lion pub Hinxton | |
| 20:30 | Transport to Holiday Inn, Whittlesford | |
| Day 3 - Wednesday 1 October - NGS variant calling and annotation | ||
| 08:30 | Transport from Holiday Inn to campus | |
| 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 | Using RNA-seq data to inform annotation with practical | Genebuild Team |
| 15:00 - 15:30 | Tea/coffee break | |
| 15:30 - 17:30 | Using RNA-seq data to inform annotation with practical (Cont.) | Genebuild Team |
| 17:30 - 18:30 | Discussion | All |
| 19:00 | Evening meal @ Red Lion pub Hinxton | |
| 20:30 | Transport to Holiday Inn, Whittlesford | |
| Day 4 - Thursday 2 October - Annotating animal genomes | ||
| 08:30 | Transport from Holiday Inn to campus | |
| 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 @ Red Lion pub Hinxton | |
| 20:30 | Transport to Holiday Inn, Whittlesford | |
| Day 5 - Friday 3 October - Functional genomics (ChIP-seq analysis) | ||
| 08:30 | Transport from Holiday Inn to campus | |
| 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 | |
Application will be via a selection process therefore applicants should be aware that, in order to be considered for place on this course, they MUST complete the online application page as well as submit a short CV, research interests and a letter of support from their supervisor or another senior co-worker explaining why they should be selected for this course. Incomplete applications will NOT be considered. Details of how to submit these extra documents will be provided on your application confirmation email.
Application registration closes 15 August 2014 (12:00 midday GMT). There will be a maximum of 30 participants on this course. Successful applicants will be notified by 29 August 2014 and will then be asked to confirm their place on the course by re-registering and paying the course fee.
Registration Fee:
£400
There is a discounted rate for members of the EMBL-EBI Industry programme (www.ebi.ac.uk/industry).
Please note that the registration fee includes:
- All meals listed in the agenda (breakfast, lunch, dinner and refreshment breaks)
- The evening meals will be at the Red Lion Pub, Hinxton.
- A USB stick and access to course materials
- Use of a computer in the EMBL-EBI IT Training Room throughout the course
- Accommodation at the Holiday Inn Whittlesford for 4 nights (29 September - 3 October 2014), plus transportation between campus and the accommodation.
To apply for this event please use the following link. Items marked * are mandatory. Incomplete applications will not be processed.