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: 

Monday April 23 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.

If you would like to be informed when applications open for this course then please click on the “Register your interest” button above.

If you would like to see details of similar course from previous years, please take a look at our course listings, using the filter boxes to refine your search by year and subject.

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

TBC

15:30-16:00

Break

 

16:00-18:30

NGS file formats practical

TBC

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

TBC

09:30-10:30

RNA-Seq and Ensembl Genebuild practical

 

10:30-11:00

Break

 

11:00-12:30

RNA-Seq analysis

TBC

12:30-13:30

Lunch

 

13:30-15:00

RNA-Seq analysis practical

TBC

15:00-15:30

Break

 

15:30-16:30

RNA-Seq analysis practical

TBC

16:30-18:30

Public databases and resources for RNA-Seq 

TBC

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

TBC

10:00-11:00

Re-sequencing and variant calling

TBC

11:00-11:30

Break

 

11:30-13:00

Re-sequencing and variant calling practical

TBC

13:00-14:00

Lunch

 

14:00-16:00

Re-sequencing and variant calling practical

TBC

16:00-16:30

Break

 

16:30-18:30

To be confirmed

TBC

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

TBC

10:30-11:30

International Genome Sample Resource

TBC

11:30-11:45

Break

 

11:45-12:45

Special topic lecture

TBC

12:45-13:00

Wrap-up and feedback

Tom Hancocks

13:00-13:30

Lunch

 

13:30

Coach to Cambridge Station