Next Generation Sequencing Workshop
This course will provide an introduction to data analyses, tools and resources for genomics and transcriptomics next generation sequence data. It will be delivered using a mixture of lectures, computer-based practical sessions and discussions with case studies from life science research.
Audience
This course is aimed at wet-lab biologists who are embarking upon research projects that will require the analysis of next generation sequence data. Some of the tools to be introduced on the course will require the use of Unix commands and the R statistics package. We strongly recommend that you familiarise yourself with these. Free tutorials are available from:
http://www.ee.surrey.ac.uk/Teaching/Unix/
http://www.r-tutor.com/r-introduction
Syllabus, Tools and Resources
During this course you will learn about:
- Genomics
- Transcriptomics
Objectives
After this course you should be able to...
. Discuss a variety of applications and workflow approaches for next generation sequence technologies
· Submit, browse and access a range of NGS data available in public repositories using EBI resources
· Use some bioinformatics software and tools to aid with the analysis of NGS data
· Appreciate some advantages and limitations of some NGS analyses.
| Time | Topic | Trainer |
|---|---|---|
| Day 1 - 14 October 2013 | ||
| 12:30 | Registration and Lunch | Laura Emery |
| 13:30 | An Introduction to the EBI and course expectations | Laura Emery |
| 14:15 | Participant introduction presentations | Participants |
| 15:00 | An introduction to NGS (lecture) | Vladimir Benes |
| 16:00 | Tea/coffee break | |
| 16:30 | NGS study design (lecture) | Vladimir Benes |
| 17:30 | Study design group activity | Laura Emery |
| 18:00 | Free time | |
| 19:00 | Course dinner | |
| Day 2 - 15 October 2013 | ||
| 09:00 | An introduction to Genomics workflow (mini lecture) | Laura Emery |
| 09:30 | DNA Assembly (hands-on) | Daniel Zerbino |
| 11:00 | Tea/coffee break | |
| 11:30 | Re-sequencing and variant calling (lecture and hands-on) | Josh Randall |
| 13:00 | Lunch and optional tour of the EMBL-EBI data centre | |
| 14:00 | Re-sequencing and variant calling (lecture and hands-on) | Josh Randall |
| 14:45 | Tea/coffee break | |
| 16:15 | Introduction to European Nucleotide Archive (ENA) - (lecture) | Marc Rosello/Rajesh Radhakrishnan |
| 17:00 | Submitting your sequences to and retrieving them from ENA (lecture and activity) | Rajesh Radhakrishnan |
| 18:00 | Genomics activity | Laura Emery |
| 18:30 | Close | |
| Day 3 - 16 October 2013 | ||
| 09:00 | RNA-seq data analysis (lecture and hands-on) | Simon Andrews |
| 11:00 | Tea/coffee break | |
| 11:30 | RNA-seq data analysis (lecture and hands-on) | Simon Andrews |
| 13:00 | Lunch and optional tour of the EMBL-EBI data centre | |
| 14:00 | Analysing RNA-Seq data with Genebuild (lecture and hands-on) | Ensembl Genebuild team |
| 15:30 | Tea/coffee break | |
| 16:00 | Exploring Transcriptomics data with ArrayExpress and Atlas (lecture and hands-on) | Functional genomics team EBI |
| 17:30 | Transcriptomics activity | Laura Emery |
| 18:00 | Close | |
| Day 4 - 17 October 2013 | ||
| 09:00 | ENCODE Project (lecture) | Steve Wilder |
| 10:00 | Tea/coffee break | |
| 10:30 | 1000 Genomes Project (lecture and hands-on) | Laura Clarke |
| 11:30 | NGS Special Lecture | Elizabeth Murchison |
| 12:30 | Course wrap-up | Laura Emery |
| 13:30 | Lunch and close | |
Registration will be via a selection process therefore applicants should be aware that, in order to be considered for a place on this course, they MUST complete the application page as well as submit a short CV, research interests. 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 16 August 2013 (12:00 midday GMT). There will be a maximum of 30 participants on this course. Successful applicants will be notified by 30 August 2013 and will then be asked to confirm their place on the course by re-registering and paying the course fee.
Please note that the registration fee of £200.00 includes:
- All meals listed in the agenda (lunch, course dinner on 14 October and refreshment breaks)
- Course materials and USB stick
- Use of a computer in the EMBL-EBI IT Training Room throughout the course
To apply for this event please use the following link. Items marked * are mandatory. Incomplete applications will not be processed.
Application is now closed
PLEASE NOTE: The successful applicants must book their own travel and accommodation.
We would recommend that you book your accommodation at any of the following locations:
Wellcome Trust Conference Centre (onsite)
Information regarding travelling to the EBI can be found here: http://www.ebi.ac.uk/about/travel