Managing and Exploring Next Generation Sequencing Data

Date:

  Tuesday 29 October 2013

Application deadline: 

Friday 25 October 2013

Contact: 

Frank O’Donnell

Registration closed

Overview

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.

During this course you will also learn about Metagenomics data standards, large-scale data management, restricted data access along with ENA resources.

You will be having an opportunity to make suggestions to shape the provision of future EBI resources especially for ENA and other related resources.

Hope you will be able to make some valuable contacts in the NGS community.

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

Additional information

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 //www.ebi.ac.uk/about/travel

Programme

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 Rossello
14:15 SRA Data Model  - Group Activity Marc Rossello
15:00 Compression: CRAM Vadim Zalunin
15:30 Tea/Coffee Break  
16:00 Data Retrieval  and ENA Browser: Presentation and Demo Nicole Silvester
18:00 Course dinner at the Wellcome Trust  
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 and feedback Tom Hancocks
13:00 Close of workshop  

How to apply

The registration deadline has been extended to 25 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.

> > > Register here > > >

Application deadline

25 October 2013

Registration closed

Organisers

Marco Punta

Tom Hancocks - EMBL-EBI, UK

Trainers

Nicole Silvester - EMBL-EBI, UK