This is a few months old but I just got around to reading this series of blog posts on next-generation sequencing (NGS) by Gabe Rudy, Golden Helix's VP of product development. This series gives a seriously useful overview of NGS technology, then delves into the analysis of NGS data at each step, right down to a description of the most commonly used file formats and tools for the job. Check it out now if you haven't already.
Part One gives an overview of NGS trends and technologies. Part Two describes the steps and programs used in the bioinfomatics of NGS data, broken down into three distinct analysis phases. Part Three gives more details on the needs and workflows of the final stage of the analysis of NGS data, or the "sense-making" phase. Finally, a fourth part is a primer on the common formats (FASTQ, SAM/BAM, VCF) and tools (BWA, Bowtie, VCFtools, SAMtools, etc) used in NGS bioinformatics and analysis.