Applied Sequencing Informatics

(4 Credits)

This course provides practical training in informatics methods for analysis of next-generation DNA sequencing (NGS) data. Students will review the development of DNA sequencing laboratory technologies and informatics tools, current methods, and promising new developments. Current best-practice bioinformatics methods will be discussed, with an emphasis on data structures and algorithms, for the most commonly used NGS technologies and applications including variant detection, ChIP-seq, RNA-seq, de novo assembly, and targeted sequencing. A number of different computational frameworks and toolkits will be used including SAMTools, BedTools, BWA, TopHat/Cufflinks, GATK, QIIME, and Galaxy.