Introduction to DNA-seq Next Generation Sequencing Analysis Workshop, November 2017

Venue: University of Leicester - College Court Conference Centre
Date: 20th, 21st November 2017
Time: 9:00am to 5:00pm each day
Organizers: Matt Blades, Chiara Batini and Ben Hunt
Admin support: Matt Blades - NGStraining@le.ac.uk
Registration:  REGISTRATION CLOSED
Participation:  Open application with selection

 

Course Overview

This two day course serves as the first in a larger two-part course in conjunction with the Exome Variants, Copy Number Calling, Variant Annotation and Reporting workshop in December 2017, as well as a standalone introduction to DNA-seq. Attendees will receive an introduction to next generation sequencing (NGS) platforms, data analysis and tools for data quality control, read alignment (mapping) and refinement using DNA-seq data. The course will conclude with a basic introduction to variant calling as a lead-in to the December workshop.

 

Audience

This course is aimed at clinicians and wet-lab biologists who are involved in research projects that will require the handling and analysis of DNA-seq data.

A significant proportion of the course will be computer-based using command line tools in the Unix environment, and applicants will find it useful to have a grasp of basic skills such as navigating the file system, making directories (e.g. pwd, cd, ls, mkdir) and managing files (e.g. cp, mv, ln, rm, less, head, tail, wc). However the morning session of the first day will include an introduction to the command line that covers all aspects needed for the course, and all commands for practical work will be given in handouts.

 

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.
•    Alignment to reference genome and BAM refinement.

 

Day 1 Overview: Introduction to NGS platforms, data formats and quality control

A range of different platforms are available for NGS, 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.

Learning objectives:

•    Develop an understanding of NGS platforms
•    Introduction to workflows
•    NGS data formats
•    QC and pre-processing of raw data

 

Day 2 Overview – Alignment and BAM refinement

Alignment to a reference genome, visualization and refinement of aligned reads, identification and mapping of genomic alterations. A basic introduction to variant calling will conclude the workshop.

Learning objectives:

•    Pre-processing of read data
•    Alignment of reads to a reference genome
•    Quality control and refinement of the aligned reads
•    Introduction to variant calling.

 

Draft workshop timetable

DNA-seq-nov-2017-schedule

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