Introduction to Next Generation Sequencing
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Date:
Tuesday 2 - Friday 5 October 2018Venue:
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication opens:
Friday 20 April 2018Application deadline:
Friday 06 July 2018Participation:
Open application with selectionContact:
Johanna LangrishRegistration fee:
£475.00Registration 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. 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:
- Basic introduction to the Unix environment:
- Introduction and exercises for Linux:
- Basic R concept 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 | Martin Pollard |
| 15:30-16:00 | Break | |
| 16:00-18:30 | NGS file formats practical | Human Genome Informatics Team |
| 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 | Leanne Haggerty & Kostas Billis |
| 09:30-11:00 | RNA-Seq and Ensembl Genebuild practical | Leanne Haggerty & Kostas Billis |
| 11:00-11:30 | Break | |
| 11:30-13:00 | RNA-Seq analysis | Simon Andrews |
| 13:00-14:00 | Lunch | |
| 14:00-16:00 | RNA-Seq analysis | Simon Andrews |
| 16:00-16:30 | Break | |
| 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 | Martin Hunt |
| 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 | |
| 16:30-17:30 | Analysis of mutational signatures in model organisms and human cancers | Nadia Volkova |
| 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 | |
| 09:00-11:00 | European Nucleotide Archive | Sam Holt |
| 11:00-11:30 | Break | |
| 11:30-12:30 | International Genome Sample Resource | Erin Haskell |
| 12:30-12:45 | Wrap-up and feedback | Tom Hancocks |
| 12:45-13:30 | Lunch | |
| 13:30 | Coach to Cambridge Station | |