Next Generation Sequencing Bioinformatics

Date:

 Monday 23 Thursday 26 September 2019

Venue: 

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

Application opens: 

Monday 25 March 2019

Application deadline: 

Friday 28 June 2019

Participation: 

Open application with selection

Contact: 

Rebecca Nicholl

Registration fee: 

£690

Registration closed

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Overview

This course will provide an introduction to the technology, analysis workflows, tools and resources for next generation sequencing data analysis. The content will provide insights into how biological knowledge can be derived from genomics experiments and explain different approaches to analysing such data. The main focus of the course will look at the assembly, re-sequencing, and variant calling undertaken during the analysis of higher-eukaryotes, with a particular emphasis on human genetic research.

Practical sessions will allow participants to process training datasets and apply appropriate statistical methods in their analyses. There will be no opportunity to work with your own data during the course.

Audience

This course is aimed at PhD students and post-doctoral researchers who are using high-throughput sequencing technologies and bioinformatics methods in their research. The content is most applicable for those working with eukaryotic genomes, human genetics and in rare disease research.

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:

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 sequencing technologies
  • Quality control methods for cleaning raw read data
  • Alignment of reads to a reference genome
  • File format conversion and processing
  • Tools for variant calling
  • Methodologies for variant annotation
  • Data resources for genomics data

Outcomes

After this course you should be able to:

  • Know the advantages and limitations of high-throughput assays
  • Assess the quality of genomic datasets
  • Compare and apply appropriate short read aligners
  • Perform variant calling analysis and variant annotation
  • Locate relevant information from online data resource

Additional information

Accommodation will be provided at the Holiday Inn, Impington Monday-Wednesday inclusive.  The course includes evening meals at the Hinxton Hall Restaurant on campus or the Red Lion Pub in nearby Hinxton village, and breaks and lunches outside the EMBL-EBI training rooms.

Programme

Day 1 – Monday 23 September 2019
12:00-13:00 Arrival, registration and lunch  
13:00-14:00 Welcome, introductions and networking Tom Hancocks
14:00-14:30 Introduction to EMBL-EBI Tom Hancocks
14:30-16:00 NGS technologies and bioinformatics basics Chiara Batini
16:00-16:30 Break  
16:30-18:00 NGS data types and quality control Chiara Batini
18:00 End of day  
18:30 Evening meal Hinxton Hall Restaurant
20:00 Shuttle to Holiday Inn, Impington  
Day 2 – Tuesday 24 September 2019
08:00 Shuttle to campus  
08:45-09:00 Arrival and registration  
09:00-11:00 Read mapping: SAM/BAM format Chiara Batini & Charles Solomon
11:00-11:30 Break  
11:30-12:30 BAM refinement Chiara Batini & Charles Solomon
12:30-13:30 Lunch  
13:30-15:30 BAM refinement Chiara Batini & Charles Solomon
15:30-16:00 Break  
16:00-17:00 BAM refinement and visualisation Chiara Batini & Charles Solomon
17:00-18:00 Using the ENA for genomics Sam Holt
18:30 Evening meal Red Lion, Hinxton
20:30 Shuttle to Holiday Inn, Impington  
Day 3 – Wednesday 25 September 2019
08:00 Shuttle to campus  
08:45-09:00 Arrival and registration  
09:00-11:00 Variant calling of SNPs Chiara Batini & Charles Solomon
11:00-11:30 Break  
11:30-12:30 Variant calling of SNPs Chiara Batini & Charles Solomon
12:30-13:30 Lunch  
13:30-14:30 Variant calling of SNPs Chiara Batini & Charles Solomon
14:30-15:30 Filtering of variants Chiara Batini & Charles Solomon
15:30-16:00 Break  
16:00-17:00 Filtering of variants Chiara Batini & Charles Solomon
17:00-18:00 Scaling things up Sean Laidlaw
18:00 End of day  
18:30 Evening meal Hinxton Hall Restaurant
20:00 Shuttle to Holiday Inn, Impington  
Day 4 – Thursday 26 September 2019
07:45 Check-out of accommodation  
08:00 Shuttle to campus  
08:45-09:00 Arrival and registration  
09:00-11:00 Annotation of variants Peter Causey-Freeman
11:00-11:30 Break  
11:30-13:00 Ensembl VEP Astrid Gall
13:00-14:00 Lunch  
14:00-15:30 Using the EVA Baron Koylass
15:30-15:45 Feedback and wrap-up Tom Hancocks
15:45 End of course  
16:00 Shuttle to Cambridge Station (Stop 5)