Introduction to Next Generation Sequencing


 Tuesday 2 Friday 5 October 2018


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

Application opens: 

Friday 20 April 2018

Application deadline: 

Friday 06 July 2018


Open application with selection


Johanna Langrish

Registration fee: 


Registration closed


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 data-sets and there will not be scope to analyse personal data. The course content makes use of data derived mainly from eukaryote model organisms - zebrafish, yeast, mice - and non-clinical human genome data.


Participants will require a basic knowledge of the Unix command line, the Ubuntu 16 operating system and the R statistical packages. We recommend these free tutorials:

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
  • NGS for transcriptomics; QC, mapping, visualisation tools
  • NGS for genomics; assembly, alignment, QC and variant calling tools
  • EMBL-EBI resources: Array Express and Expression Atlas, ENA and the CRAM toolkit, International Genome Sample Resource


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 - Tuesday 02 October 2018
12:00-13:00 Arrival, registration and lunch  
13:00-14:00 Introduction to EMBL-EBI and networking activities Tom Hancocks
14:00-14:30 Overview of NGS technologies Tom Hancocks
14:30-15:30 Overview of NGS bioinformatics Martin Pollard
15:30-16:00 Break  
16:00-18:30 NGS file formats practical Human Genome Informatics Team
18:30 End of day  
18:45 Check in to accommodation Conference Centre Reception
19:30 Evening meal Hinxton Hall Restaurant
Day 2 - Wednesday 03 October 2018
08:45 Arrival  
09:00-09:30 RNA-Seq and Ensembl Genebuild Leanne Haggerty & Kostas Billis
09:30-11:00 RNA-Seq and Ensembl Genebuild practical Leanne Haggerty & Kostas Billis
11:00-11:30 Break  
11:30-13:00 RNA-Seq analysis Simon Andrews
13:00-14:00 Lunch  
14:00-16:00 RNA-Seq analysis Simon Andrews
16:00-16:30 Break  
16:30-18:30 Public databases and resources for RNA-Seq  Laura Huerta
18:30 End of day  
19:00 Evening meal Hinxton Hall Restaurant
Day 3 - Thursday 04 October 2018
08:45 Arrival  
09:00-10:00 De novo genome assembly Martin Hunt
10:00-11:00 Re-sequencing and variant calling Human Genetics Informatics Team
11:00-11:30 Break  
11:30-13:00 Re-sequencing and variant calling practical Human Genetics Informatics Team
13:00-14:00 Lunch  
14:00-16:00 Re-sequencing and variant calling practical Human Genetics Informatics Team
16:00-16:30 Break  
16:30-17:30 Analysis of mutational signatures in model organisms and human cancers Nadia Volkova
18:30 End of day  
19:00 Evening meal Red Lion, Hinxton
Day 4 -  Friday 05 October 2018
08:30 Checkout of accommodation Conference Centre Reception
08:45 Arrival  
09:00-11:00 European Nucleotide Archive Sam Holt
11:00-11:30 Break  
11:30-12:30 International Genome Sample Resource Erin Haskell
12:30-12:45 Wrap-up and feedback Tom Hancocks
12:45-13:30 Lunch  
13:30 Coach to Cambridge Station