Project Description

Dr Felicity Newell

 

QIMR Berghofer Medical Research Institute

NGS mapping, errors and quality control

Next generation sequencing & bioinformatics

Monday 1 July 2019

Felicity received her PhD from The University of Queensland in 2007, and completed a Master of Information Technology at the Queensland University of Technology in 2009. She has worked as a bioinformatics programmer, developing biological web applications at QFAB and software for the analysis of cancer sequencing data at the Queensland Centre for Medical Genomics at UQ. She has also conducted postdoctoral research at UQ and QUT, using bioinformatics approaches to study cancer and autoimmune diseases. She is currently a Senior Research Officer within the Medical Genomics group at QIMR Berghofer Medical Research Institute where her research involves using next generation sequencing data to understand the genetics of cancers including oesophageal adenocarcinoma and melanoma.

The analysis of next generation sequencing data often requires alignment (mapping) of the reads that are generated to a reference genome. Alignment software needs to be able to efficiently identify the location of reads within a reference genome while accounting for sequence variation, including true variation such as single nucleotide polymorphisms, as well as differences that are introduced as the result of sequencing errors. In this presentation, I will give an overview of some of the approaches to sequence alignment. A good understanding of the common errors and biases that can occur with mapping and throughout NGS processing pipelines is necessary in order to obtain high quality data from downstream analyses such as variant detection. I will also discuss the sources of such errors and outline quality control steps that may be performed.