Introduction to Next Generation Sequencing
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Date:
Monday 9 - Thursday 12 April 2018Venue:
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication opens:
Wednesday 25 October 2017Application deadline:
Friday 12 January 2018Participation:
Open application with selectionContact:
Johanna LangrishRegistration 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:
- Basic introduction to the Unix environment:
www.ee.surrey.ac.uk/Teaching/Unix - Introduction and exercises for Bio-Linux 7:
http://nebc.nerc.ac.uk/support/training/course-notes/past-notes/intro-bl7 - Basic R concept tutorials:
www.r-tutor.com/r-introduction
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 |