Introduction to Next Generation Sequencing (April)


 Monday 4 Thursday 7 April 2016


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

Application opens: 

Tuesday October 20 2015

Application deadline: 

Friday January 08 2016


Open application with selection

Registration fee: 

£495 (Includes 4 days accommodation & food)

Registration closed

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This course will provide an introduction to the technology, data analysis, tools and resources for next generation sequencing (NGS) data. The content is intended to provide a broad overview of the subject areas, and to highlight key resources, approaches and methodologies. Topics will be delivered using a mixture of lectures, practical sessions and open discussions. Practical work during the course will use small, example datasets and there will not be scope to analyse personal data.


This course is aimed at wet-lab biologists who are embarking upon research projects that will involve NGS and the analysis of the data generated.

Participants will require a basic knowledge of the Unix command line, Bio-Linux and the R statistical package. We recommend these free tutorials:

Please note: participants without basic knowledge of these resources will have difficulty in completing the practical sessions.

Syllabus, tools and resources

During this course you will learn about:

  • NGS platforms and NGS data files and formats
  • NGS bioinformatics workflow steps following sequence generation
  • Experimental NGS design and planning for your bioinformatics needs
  • NGS for genomics; assembly, alignment, QC and variant calling tools
  • NGS for transcriptomics; QC, mapping, visualisation tools
  • EMBL-EBI resources: Array Express and Expression Atlas, ENA and the CRAM toolkit


After this course you should be able to:

  • Discuss a variety of applications and workflow approaches for NGS technologies
  • Use a range of bioinformatics software and tools to undertake basic analysis of NGS data
  • Understand the advantages and limitations of NGS analyses
  • Submit, browse and access a range of NGS data available in public repositories using EBI resources


Time Topic Trainer
Day 1 - 4 April
12:00 - 13:00 Registration and Lunch  
13:00 - 13:30 Welcome to EMBL-EBI  Tom Hancocks
13:30 - 14:00 Introduction and networking activitie Tom Hancocks
14:00 - 15:00 Overview of NGS technologies Tom Hancocks
15:00 - 15:30 Break   
15:30 - 18:00 Overview of NGS bioinformatics  Joshua Randall
19:00 Evening meal Hinxton Hall 
Day 2 - 5 April
09:00 - 09:30 RNA-Seq and Ensembl Genebuild  John Collins
09:30 - 10:30  Ensembl Genebuild RNA-Seq practical John Collins, Daniel Murphy and Konstantinos Billis 
10:30 - 11:00 Break  
11:00 - 12:30 RNA-Seq analysis Simon Andrews
12:30 - 13:30 Lunch  
13:30 - 15:00 RNA-Seq analysis practical  Simon Andrews
15:00 - 15:30 Break  
15:30 - 16:30 RNA-Seq analysis practical Simon Andrews
16:30 - 18:00 Array Express & Expression Atlas Anja Füllgrabe and Melissa Burke 
19:00 Evening meal Hinxton Hall
Day 3 - 6 April 
09:00 - 10:30 Read assembly Martin Hunt and Gavin Rutledge 
10:30 - 11:00 Break  
11:00 - 12:00 Read assembly  Martin Hunt and Gavin Rutledge 
12:00 - 12:30 Introduction to the European Nucleotide Archive Marc Rossello
12:30 - 13:30 Lunch   
13:30 - 15:00 Re-sequencing and variant calling  Joshua Randall
15:00 - 15:30 Break  
15:30 - 18:00 Re-sequencing and variant calling Joshua Randall
19:00 Evening meal Hinxton Hall
Day 4 - 7 April
09:00 - 10:00 ENA for your NGS workflow   Marc Rossello
10:00 - 10:30 Break  
10:30 - 11:30 1000 Genome Project and beyond Susan Fairley 
11:30 - 12:30 Exploring the landscape of pharmacogenomic interactions in cancer Francesco Iorio
12:30 - 13:00 Discussion and feedback   
13:00 - 14:00 Lunch and end of course  
14:15 Bus to Cambridge Railway Station   
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.


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 PDF document to containing a short biography including your work history and a description of your current research interests. Each document should be no longer than 150 words.
  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

08 January 2016

Number of places

30 places

Registration closed

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Tom Hancocks

Marc Rossello

Joshua Randall


Tom Hancocks - EMBL-EBI, UK

Joshua Randall - Sanger Institute

John Collins - Wellcome Trust Sanger Institute

Daniel Murphy - EMBL-EBI, UK

Kostas Billis - EMBL-EBI, UK

Simon Andrews - Babraham Institute

Anja Fullgrabe - EMBL-EBI, UK

Melissa Burke - EMBL-EBI, UK

Martin Hunt - Sanger Institute

Gavin Rutledge - Sanger Institute

Marc Rossello - EMBL-EBI, UK

Susan Fairley - EMBL-EBI, UK

Francesco Iorio - EMBL-EBI, UK