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 October 25 2017

Application deadline: 

Friday January 12 2018

Participation: 

Open application with selection

Registration fee: 

£560 - (Including Accommodation)

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 Josh Randall
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  
12:30 Bus to accommodation  
Day 3 - Wednesday 11 April 2018
08:30 Bus to campus  
09:00 - 10:30 Genome assembly Zemin Nim
10:30 - 11:00 Break  
11:00 - 12:00 Genome assembly  Zemin Nim & Francesca Giordano
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 - 18:30 Re-sequencing and variant calling practical Human Genetics Informatics Team
19:30 Evening meal at Red Lion, Hinxton  
21:00 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 Marc Rossello
10:00 - 10:30 Break  
10:30 - 11:30 International Genome Sample Resource Emily Perry
11:30 - 12:30 Special lecture: Identifying and characterising cell-types with single-cell RNA sequencing Tallulah Andrews
12:30 - 12:45 Feedback and wrap-up Tom Hancocks 
12:45 - 13:30 Lunch  
13:30 Bus to Whittlesford Parkway and Cambridge Station