Managing and Exploring Next Generation Sequencing Data
This workshop is supported by the European Sequencing and Genotyping Infrastructure (ESGI) project funded under the FP7 programme of the European Commission: http://www.esgi-infrastructure.eu/
This workshop covers submission and retrieval services provided by the EMBL-EBI's European Nucleotide Archive – www.ebi.ac.uk/ena – for raw and early analysis data from next generation nucleotide sequencing platforms. It will also cover emerging efficient data compression technologies.
Audience
Scientists working with next generation sequencing platforms that require knowledge in handling, manipulation and storage of large sequence datasets.
Syllabus, Tools and Resources
During this course you will learn about:
- Data formats, compression technology, standards
- Data upload tools, submission services
- Data search and retrieval via text, advanced and sequence similarity search
Learning Objectives
After this course you should be able to:
- Move data around using different tools
- Submit data to ENA SRA using different submission systems
- Data handling requirements for controlled access data
- Understand the different types of data that can be retrieved from ENA and how to find/download them
| Time | Topic | Trainer |
|---|---|---|
| Day 1 - Tuesday 29 October 2013 | ||
| 12:00 | Registration and Lunch | |
| 13:30 | EBI Introduction | Rajesh Radhakrishnan |
| 13:45 | ENA and SRA Introduction | Marc Rosello |
| 14:15 | Compression: CRAM | Vadim Zalunin |
| 14:45 | SRA Data Model - Group Activity | Marc Rosello |
| 15:30 | Tea/Coffee Break | |
| 16:00 | Data Retrieval and ENA Browser: Presentation and Quiz | Nicole Silvester |
| 17:30 | Workshop Dinner | |
| Day 2 - Wednesday 30 October 2013 |
||
| 09:00 | SRA Submissions: Presentation and Practical | Rajesh Radhakrishnan |
| 10:30 | Tea/Coffee Break | |
| 11:00 | EGA: Accessing and submitting controlled access data | Jeff Almeida-King |
| 12:30 | Workshop wrap-up | Tom Hancocks |
| 13:00 | Close of workshop | |
Please note this agenda is a draft agenda and therefore subject to change.
Registration closes 15 October 2013 (12:00 midday GMT).
Please note that the registration fee of £100.00 includes:
- All meals listed in the agenda (lunch, course dinner on 29 October and refreshment breaks)
- Course materials and USB stick
- Use of a computer in the EMBL-EBI IT Training Room throughout the course
To register to attend this event please use the following link. Items marked * are mandatory. Incomplete applications will not be processed.A credit/debit card will be required at the time of registering as a complete payment is required at the time of registration.
If you require accommodation, please ensure you arrange this well in advance. Accommodation is not included in this workshop.
We would recommend you book accommodation with the Wellcome Trust Conference Centre
You will need to book this as soon as possible as availability is often limited.
Please contact their reception, Tel: +44 (0) 1223 495000 or email: reception@wtconference.org.uk
or you can book with The Red Lion, Hinxton, Cambridgeshire CB10 1QY, (Tel: +44(0) 1799 530601) which has 8 rooms available.
Alternatively you can contact the Holiday Inn Express Duxford 42 Station Road, East Whittlesford Bridge, Cambridge CB22 4NL (located next to Whittlesford Train Station) (Tel: +44(0) 1223 497070) which has 75 rooms available.
Details regarding travel to the EBI can be found here http://www.ebi.ac.uk/about/travel