Analysis of Next-Generation Sequencing Data

Next generation DNA sequencing technology has revolutionized our ability to ask almost any question of our genome, epigenome or transcriptome. In Part I of the course, we focus on the principles of the dominant technology: the Illumina short read sequencing by synthesis platform. The complete analysis pipeline is examined in detail, from the generation of raw reads, through alignment to the genome (Part II), and up to gene-centric analyses in Part III. At each step, there will be a strong emphasis on quality control, highlighting limitations and common pitfalls of the most commonly used tools, as well as ways to deal with them. In Part IV, alternate DNA sequencing technologies are surveyed, showcasing their applications.
Students will use the knowledge gained throughout this course to apply to a practical project which will focus on the analysis of one or more NGS data types to address a biomedically relevant question.