Introduction to Next Generation Sequencing

Date:

 Monday 9 Thursday 12 April 2018

Venue: 

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

Application opens: 

Wednesday 25 October 2017

Application deadline: 

Friday 12 January 2018

Participation: 

Open application with selection

Contact: 

Johanna Langrish

Registration fee: 

£560 - (Including Accommodation)

Registration closed

Overview

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.

Audience

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
  • 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

Outcomes

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

Programme

Time Topic Trainer
Day 1 - Monday 09 April 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 Genetics Informatics Team
19:00 Evening meal at Hinxton Hall   
20:30 Bus to accommodation   
Day 2 - Tuesday 10 April 2018
08:40 Bus to campus  
09:00 - 09:30 RNA-Seq and Ensembl Genebuild John Collins
09:30 - 10:30 Ensembl Genebuild practical John Collins, Kostas Billis, Osagie Izugu
10:30 - 11:00 Break  
11:00 - 12:30 RNA-Seq analysis Laura Biggins
12:30 - 13:30 Lunch  
13:30 - 15:00 RNA-Seq analysis practical Laura Biggins 
15:00 - 15:30 Break  
15:30 - 16:30 RNA-Seq Analysis practical Laura Biggins
16:30 - 18:30 Public databases and resources for RNA-seq  Laura Huerta
19:00 Evening meal at Hinxton Hall  
20:30 Bus to accommodation  
Day 3 - Wednesday 11 April 2018
08:30 Bus to campus  
09:00 - 10:30 Genome assembly - Overview video, discussion and materials Tom Hancocks
10:30 - 11:00 Break  
11:00 - 11:45 Introduction to the European Nucleotide Archive Ana Toribio
11:45 - 12:30 Re-sequencing and variant calling Human Genetics Informatics Team
12:30 - 13:30 Lunch  
13:30 - 15:00 Re-sequencing and variant calling Human Genetics Informatics Team
15:00 - 15:30 Break  
15:30 - 18:30 Re-sequencing and variant calling practical Human Genetics Informatics Team
19:00 Evening meal at Red Lion, Hinxton  
21:30 Bus to accommodation  
Day 4 - Thursday 12 April 2018
08:15 Check-out  
08:30 Bus to campus  
09:00 - 10:30 ENA for your NGS workflow Ana Toribio
10:00 - 10:30 Break  
10:30 - 11:30 International Genome Sample Resource Emily Perry
11:30 - 12:30 Single-cell RNA sequencing Vladimir Kiselev
12:30 - 12:45 Feedback and wrap-up Tom Hancocks 
12:45 - 13:30 Lunch  
13:30 Bus to Cambridge Station