This is a SciLifeLab/NBIS course covering an introduction to computational methods for NGS. The course will provide an entry-level introduction to a wide range of analytical techniques for massively parallel sequencing, including basic linux commands. We will pair lectures on the theory of analysis algorithms with practical computational exercises demonstrating the use of common tools for analyzing data from each of several common sequencing study designs. Topics covered will include: • Basic Linux usage • NGS read-to-reference alignment (genomic and RNA-Seq) • Variant calling in populations • RNA-Seq expression analysis