Exploring genomic variation with high throughput sequencing data

Date:

 Monday 28 November - Thursday 1 December 2016

Venue: 

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

Application opens: 

Friday 01 July 2016

Application deadline: 

Friday 23 September 2016

Participation: 

Open application with selection

Contact: 

EMBL-EBI Training Team

Registration fee: 

£400

Registration closed

Overview

The aim of this course is to familiarise participants with the analysis and interpretation of human genome sequence variation data derived from high-throughput sequencing applications.

Audience

This course is aimed at PhD students and post-doctoral researchers who are already applying, or planning to use, high-throughput sequencing (HTS) technologies and bioinformatics methods in their research.

Familiarity with the technology and biological use cases of HTS would be beneficial, as well as knowledge of R/Bioconductor and the Unix/Linux operating system.

Outcomes

At the end of the course you will be familiar with NGS data analysis methodologies for variant detection and will be able to access and explore appropriate variation resources and use them to retrieve relevant variant information.

Programme

Time Topic Trainer
Day 1 - 
12:00 - 13:00 Registration and lunch  
13:00 - 14:00 Welcome and Introduction  Chiara Batini
14:00 - 15:30 Lecture: Introduction to NGS technologies and library preparation  Chiara Batini
15:30 - 15:45 Tea/coffee break  
15:45 - 17:30 Lecture and practicals: Introduction to data types and data QC  Matthew Blades
17:30 - 18:00 Recap  
19:00 Evening meal  
Day 2 - 
09:00 - 09:30 Recap session  
09:30 - 11:00 Lecture and practicals: Mapping; SAM/BAM format  Chiara Batini
11:00 - 11:15 Tea/coffee break  
11:15 - 13:00 Lecture and practicals: BAM refinement [Local Realignment, Base quality recalibration]  Chiara Batini
13:00 - 14:00 Lunch  
14:00 - 16:00 Lecture and practicals: BAM refinement [Duplicate removal, BAM handling, BAM visualization]  Chiara Batini
16:00 - 16:45 Tea/coffee break  
16:45 - 17:30 Lecture and practicals: BAM refinement [Duplicate removal, BAM handling, BAM visualization]  Chiara Batini
17:30 - 18:00 Recap session  
19:00 Evening meal  
Day 3 - 
09:00 - 09:30 Recap session  
09:30 - 11:15 Lecture and practicals: Variant calling - SNPs  Chiara Batini
11:15 - 11:30 Tea/coffee break  
11:30 - 13:00 Lecture and practicals: Filtering variants  Chiara Batini
13:00 - 14:00 Lunch  
14:00 - 15:30 Lecture and practicals:  Ensembl VEP  Will McLaren
15:30 - 15:45 Tea/coffee break  
15:45 - 17:30 Lecture and practicals:  EVA  Gary Saunders
17:30 - 18:00 Recap session  
19:00 Evening meal  
Day 4 - 
09:00 - 10:00 Principle and methods for linking genotype to phenotype  Oliver Stegle
10:00 - 10:30 Tea/coffee break  
10:30 - 13:00 Hands on  Oliver Stegle
13:00 Feedback and end of course  
13:30 Bus back to Cambridge  
European Bioinformatics Institute (EMBL-EBI)
Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom

At EMBL-EBI, we manage the world’s public biological data and make it freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. Set on the beautiful Wellcome Genome Campus near Cambridge in the UK, we support scientists throughout the world in seeking solutions to challenges in healthcare, agriculture and the environment.

/training/events/0000/files/content.ebi.ac.uk/venues/south_building_exterior.jpg

In association with

How to apply

In order to be considered for a place on this course, applicants must do the following:

  1. Complete the online application form.
  2. Submit a WORD document to frank@ebi.ac.uk containing a short biography including your work history, a description of your current research interestsand a short biography. Each document should be no longer than 100 words and written in paragraph form.
  3. Provide a letter of support from a supervisor or a senior co-worker explaining why you should be selected for this course.

Further details will be provided on your confirmation email after completing the online form.

Incomplete applications will NOT be considered. Please read through the following guidance document for more information on how to complete your application.

 

Application deadline

23 September 2016

Number of places

30 places

Registration closed

Organisers

Gabriella Rustici - University of Cambridge, UK

Sarah Morgan - EMBL-EBI, UK

Trainers

Gary Saunders - EMBL-EBI, UK

Oliver Stegle - EMBL-EBI, UK

Chiara Batini - University of Leicester

Matthew Blades - University of Leicester

Will McLaren - EMBL-EBI, UK