Next Generation Sequencing workshop January 2015
Venue: University of Leicester
Date: 7th, 8th and 9th January 2015
Time: 9:30am to 5:00pm each day
Organizers: Matthew Blades, Kate Lee and Chiara Batini
Admin support: Kate Lee
Registration opens: 31st October
This course will provide an introduction to next generation sequencing platforms, data analysis and tools for data quality control, genome assembly and variant calling. The course will be delivered using a mixture of lectures and computer based hands on practical sessions, with discussions using case studies from life science research at Leicester University.
This course is aimed at wet-lab biologists who are embarking upon research projects that will require the handling and analysis of next generation sequencing data.
A significant proportion of the course will be computer-based using command line tools in the Unix environment, therefore, in order to gain maximum benefit from the course all attendees will be required to have basic unix skills. This means applicants must at a minimum be able to move easily around the file sytem and make directories (e.g. pwd, cd, ls, mkdir), manage files (e.g. cp, mv, ln, rm, less, head, tail, wc) and search with grep.
IT services will be running an ‘Introduction to Linux’ course before the workshop specifically for University of Leicester attendees of the BBASH RNA-seq course on the 10th December. If you are selected to attend the workshop and are not an experienced unix user, then a place will be reserved for you.
Registration is closed.
During this course you will learn about:
• The commonly used NGS platforms and data output files.
• Quality control and filtering of raw read data (FASTQC and FastxToolkit)
• De-novo genome assembly using Velvet, parameter optimization and analysis of assembly quality
• Alignment to reference genome and variant calling using bwa and samtools
Day 1 Overview: Introduction to NGS platforms, data formats and quality control
A range of different platforms are available for next generation sequencing, these will be described and the key advantages/disadvantages discussed. The commonly used output data file formats and workflows will be discussed along with a practical session illustrating a workflow for quality control and filtering of raw read data.
• Develop an understanding of NGS platforms
• Introduction to workflows
• NGS data formats
• QC and pre-processing of raw data
Day 2 Overview – De-novo Genome Assembly using Velvet
Velvet is a tool that can be used for assembly of genomes from NGS data. This session will consist of an introduction to Velvet, followed by hands-on exercises using short and long read data. The effect and importance of good quality read data will be investigated, along with Velvet parameters and methods to optimize these. The quality of the assembly will then be assessed.
• Pre-processing of read data
• De-novo genome assembly using Velvet
• Assessment and optimisation of Velvet parameters
• Assessment of assembly quality
Day 3 Overview – Aligning reads to a reference and Variant Calling
Align reads to a reference and Identify and map genomic alterations, including single nucleotide polymorphisms and short indels. Commonly occurring errors will be considered and filtered out.
• Alignment to reference genome using bwa
• Visualization of aligned reads
• Quality control and refinement of the aligned reads
• Variant calling and filtering using samtools