Animal Genome Informatics

Date:

 Monday 29 September Friday 3 October 2014

Venue: 

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

Application deadline: 

Friday August 15 2014

Participation: 

Open application with selection

Contact: 

Frank O’Donnell

Registration fee: 

£400

Registration closed

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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