Introduction to Next Generation Sequencing (October)


 Monday 9 Thursday 12 October 2017


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

Application opens: 

Friday April 28 2017

Application deadline: 

Friday July 28 2017


Open application with selection


Johanna Langrish

Registration fee: 


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 and the R statistical package. We recommend these free tutorials:

Participants without basic knowledge of these resources will have difficulty in completing the practical sessions. We strongly recommend that you make every effort to access these materials and other training available online or within your host institute to best prepare you for the course.

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

Additional information

The course price includes 3 nights accommodation at the Wellcome Genome Campus Conference Centre and catering for the duration of the course. A bus is provided to take participants to Cambridge Railway Station after the course. Please see Travel to EMBL-EBI for futher information on your journey to the campus.


Time Topic Trainer
Day 1 - Monday 09 October 2017
12:00 - 13:00 Arrival, Registration and lunch  
13:00 - 13:30 Welcome and introduction to EMBL-EBI Tom Hancocks
13:30 - 14:30 Introductions and networking activities  Tom Hancocks 
14:30 - 15:30 Overview of NGS technologies Tom Hancocks 
15:30 - 16:00 Break  
16:00 - 17:00 Overview of NGS bioinformatics  Martin Pollard
17:00 - 18:30 NGS data formats practical Human Genome Informatics Team
18:30 End of day  
19:30 Dinner at Hinxton Hall  
Day 2 - Tuesday 10 October 2017
08:45 Arrival  
09:00 - 09:30 RNA-Seq and Ensembl Genebuild John Collins
09:30 - 10:30 Ensembl Genebuild RNA-Seq practical Kostas Billis, Osagie Izuogu, Fergal Martin & John Collins
10:30 - 11:00 Break  
11:00 - 12:30 RNA-Seq analysis Simon Andrews
12:30 - 13:30 Lunch  
13:30 - 16:00 RNA-Seq analysis practical Simon Andrews
16:00 - 16:30 Break  
16:30 - 18:00 Public databases and resources for RNA-seq Laura Huerta-Martinez
18:00 - 18:30 Introduction to ENA Marc Rossello
19:00 Dinner at Hinxton Hall  
Day 3 - Wednesday 11 October 2017
08:45 Arrival  
09:00 - 10:30 Genome assembly Zemin Ning
10:30 - 11:00 Break  
11:00 - 12:00 Genome assembly practical Zemin Ning & Francesca Giordano
12:00 - 13:00 1000 Genomes Project Emily Perry
13:00 - 14:00 Lunch  
14:00 - 15:00 ENA for NGS workflows Marc Rossello
15:00 - 16:00 Read alignment Anthony Doran
16:00 - 16:30 Break  
16:30 - 18:30 Read alignment practical Anthony Doran
19:30 Dinner at the Red Lion Pub, Hinxton  
Day 4 - Thursday 12 October 2017
08:45 Arrival  
09:00 - 10:30 Structural variant calling Thomas Keane
10:30 - 11:00  Break  
11:00 - 12:30 Structural variant calling practical Thomas Keane
12:30 - 12:45 Feedback and wrap-up
Tom Hancocks
12:45 - 13:25 Lunch  
13:30 Bus to Cambridge Railway Station