Introduction to Next Generation Sequencing
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Date:
Tuesday 28 - Friday 31 October 2014Venue:
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomParticipation:
Open application with selectionContact:
Frank O’DonnellRegistration fee:
£495Registration closed
Overview
This course will provide an introduction to technology, data analysis, tools and resources for next generation sequencing (NGS) data. The content is intended to provide a broad overview of the subject area, and to highlight key resources, approaches and methodologies. Topics will be delivered using a mixture of lectures, practical sessions and group discussions. Analysis work during the course will use small, example datasets 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 basic knowledge of the Unix command line, Bio-Linux 7 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, the Linux environment we will be using during the course: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
- 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 - Baseline Atlas, CRAM toolkit and ENA - used for further work, data management and sequence submissions
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 28 October 2014 | ||
| 12:00 - 13:00 | Registration and Lunch | |
| 13:00 - 13:30 | Welcome to EMBL-EBI | Tom Hancocks |
| 13:30 - 14:00 | Introduction and networking activities | Tom Hancocks |
| 14:00 - 15:00 | Overview of NGS technologies | Tom Hancocks |
| 15:00 - 15:30 | Tea/Coffee | |
| 15:30 - 17:30 | Overview of NGS bioinformatics | Josh Randall |
| 19:00 | Dinner at Hinxton Hall (on campus) | |
| Day 2 - Wednesday 29 October 2014 | ||
| 09:00 - 10:30 | Read assembly | Daniel Zerbino |
| 10:30 - 11:00 | Tea/coffee | |
| 11:00 - 12:00 | Read assembly | Daniel Zerbino |
| 12:00 - 12:30 | European Nucleotide Archive | Marc Rossello |
| 12:30 - 13:30 | Lunch | |
| 13:30 - 15:00 | Re-sequencing and variant calling | Josh Randall |
| 15:00 - 15:30 | Tea/Coffee | |
| 15:30 - 18:00 | Re-sequencing and variant calling | Josh Randall |
| 19:00 | Dinner at Hinxton Hall (on campus) | |
| Day 3 - Thursday 30 October 2014 | ||
| 09:00 - 09:30 | RNA-Seq and Ensembl Genebuild | John Collins |
| 09:30 - 10:30 | Genebuild RNA-Seq analysis practical | Rishi Nag, Dan Murphy |
| 10:30 - 11:00 | Tea/Coffee | |
| 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 | Tea/Coffee | |
| 15:30 - 17:00 | RNA-Seq analysis practical | Simon Andrews |
| 17:00 - 18:00 | Array Express & Expression Atlas | Amy Tang |
| 19:00 | Dinner at Hinxton Hall (on campus) | |
| Day 4 - Friday 31 October 2014 | ||
| 09:00 - 10:00 | ENA for your NGS workflow | Marc Rossello |
| 10:00 - 10:30 | Tea/coffee break | |
| 10:30 - 11:30 | 1000 Genomes Project | Laura Clarke |
| 11:30 - 12:30 | NGS Special lecture | Elizabeth Murchison |
| 12:30 - 13:00 | Discussion and feedback | Tom Hancocks |
| 13:00 | Lunch and end of course | |
| 14:15 | Bus to Cambridge train station | |
Course materials for download: