Introduction to Next Generation Sequencing (April)

Date:

 Monday 3 Thursday 6 April 2017

Venue: 

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

Application opens: 

Wednesday October 12 2016

Application deadline: 

Friday January 06 2017

Participation: 

Open application with selection

Contact: 

Johanna Langrish

Registration fee: 

£550

Registration closed

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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
  • 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

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 - 3 April 2017 - Introduction
12:00 - 13:00 Registration and lunch  
13:00 - 13:30 Welcome to EMBL-EBI Tom Hancocks
13:30 - 14:00 Introductions and networking activities  Tom Hancocks 
14:00 - 15:00 Overview of NGS technologies Tom Hancocks
15:00 - 15:30 Break  
15:30 - 18:00

Overview of NGS bioinformactis

Joshua Randall
19:00 Evening meal at Hinxton Hall  
20:30 Shuttle to accommodation  
Day 2 - 4 April 2017 - NGS for Transcriptomics
08:45 Shuttle to Wellcome Genome Campus  
09:00 - 09:30 RNA-Seq and Ensembl Genebuild

John Collins

09:30 - 10:30

Ensembl Genebuild RNA-Seq practical

Dan Murphy 
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

Public databases and resources for RNA-seq

Amy Tang 
19:00 Evening meal at Hinxton Hall  
20:30 Shuttle to accommodation  
Day 3 - 5 April 2017 - NGS for Genomics
08:45 Shuttle to Wellcome Genome Campus  
09:00 - 10:00 Read Assembly and Genome Reference Consortium Kerstin Howe
10:00 - 10:30 Read Assembly practical All
10:30 - 11:00 Break  
11:00 - 12:00 Introduction to the European Nucleotide Archive

Marc Rosello

12:00 - 12:30 Re-sequencing and variant calling Joshua Randall
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 at Red Lion, Hinxton

 
20:30

Shutte to accommodation

 
Day 4 - 6 April 2017 - Using NGS Resources
08:45 Shuttle to Wellcome Genome Campus  
09:00 - 10:00 ENA for your NGS workflow Marc Rosello
10:00 - 10:30 Break   
10:30 - 11:30 1000 Genomes, and beyond ... Susan Fairley 
11:30 - 12:30

HipSci project

Ian Streeter
12:30 - 12:45 Discussion and feedback  Tom Hancocks
12:45 - 13:30 Lunch and end of course  
13:30 Coach to Whittlesford Parkway & Cambridge Railway Station