The following links should be help as a review or an introduction to concepts and terminology related to next-generation sequencing:
A basic review of the sequencing process.
Sequencing technologies, the next generation, (M. Metzker, Nature Reviews - Genetics)
An excellent, detailed overview of the myriad next-gen sequencing methdologies.
Next-generation sequencing: adjusting to data overload (M. Baker, Nature Methods)
A nice piece explaining the problems inherent in trying to analyze terabytes of data. The GATK addresses this issue by requiring all datasets be in reference order, so only small chunks of the genome need to be in memory at once, as explained here.
Primer on NGS analysis, from Broad Institute Primers in Medical Genetics
