Introduction to Next Generation Sequencing

Date:

 Tuesday 2 Friday 5 October 2018

Venue: 

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

Application opens: 

Friday April 20 2018

Application deadline: 

Friday July 06 2018

Participation: 

Open application with selection

Contact: 

Johanna Langrish

Registration fee: 

£475.00

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. The course content makes use of data derived mainly from eukaryote model organisms - zebrafish, yeast, mice - and non-clinical human genome data.

Audience

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

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 - 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

To be confirmed

15:30-16:00

Break

 

16:00-18:30

NGS file formats practical

To be confirmed

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

To be confirmed

09:30-10:30

RNA-Seq and Ensembl Genebuild practical

 

10:30-11:00

Break

 

11:00-12:30

RNA-Seq analysis

Babraham Bioinformatics

12:30-13:30

Lunch

 

13:30-15:00

RNA-Seq analysis practical

Babraham Bioinformatics

15:00-15:30

Break

 

15:30-16:30

RNA-Seq analysis practical

Barbaham Bioinformatics

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

To be confirmed

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

 

16:30-18:30

To be confirmed

To be confirmed

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

 

09:00-10:00

To be confirmed

To be confirmed

10:30-11:30

International Genome Sample Resource

To be confirmed

11:30-11:45

Break

 

11:45-12:45

Special topic lecture

To be confirmed

12:45-13:00

Wrap-up and feedback

Tom Hancocks

13:00-13:30

Lunch

 

13:30

Coach to Cambridge Station