Next-generation sequencing methods offer decreased cost, increased throughput, and the potential for obtaining new biological insights. However, analyzing the gigabytes of data produced by these methods poses a number of challenges. In this tutorial, we provide a brief introduction to next gen sequencing techniques, the type of data they produce, and the types of information that users of this technology typically hope to extract from this data. We will also provide an introduction to tools that can be used to analyze next gen data. This discussion will mainly focus on tools available in R, but will also briefly discuss standalone tools and tools available in other packages, e.g., MATLAB.