Next-generation Sequencing (NGS) is one of the fundamental technological developments of the decade in life sciences. Whole Genome Sequencing (WGS), RAD-Seq, RNA-Seq, Chip-Seq, and several other technologies are routinely used to investigate important biological problems. These are also called high-throughput sequencing technologies with good reason: they generate vast amounts of data that need to be processed. NGS is the main reason for computational biology becoming a "big data" discipline. More than anything else, this is a field that requires strong bioinformatics techniques. There is a very strong demand for professionals with these skillsets.

Here, we will not discuss each individual NGS technique per se (this will require a whole book on its own). We will use an existing WGS dataset and the human 1000 genomes project to illustrate the most common steps necessary to analyze genomic data. The recipes presented here will be easily applicable for other genomic sequencing...