Dr Felicity Newell
QIMR Berghofer Medical Research Institute
NGS mapping, errors and quality control
Next generation sequencing & bioinformatics
Monday 2 July 2018
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. Current NGS platforms are capable of generating a large number of reads that may be short in length and will contain sequence differences when compared to the reference. These differences will be the result of true variation, for example, single nucleotide polymorphisms, as well as differences that are introduced as the result of sequencing errors. Alignment software therefore needs to be able to efficiently identify the location of reads within a reference genome while accounting for such sequence variation. In this presentation, I will give an overview of some of the approaches to sequence alignment and give examples of tools that are used. A good understanding of the common errors and biases that can occur with mapping 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 the quality control steps that may be performed in order to address these issues.