Check the tutorial section for a head start.

Few posts:

• Challenges and Solutions in the Analysis of Next Generation Sequence Data
• Tutorial: Workshop - Analysis of Next Generation Sequencing Data
• Tutorial: High Throughput Sequence Analysis with R and Bioconductor
• Tutorial: Introduction to NGS Bioinformatics by the Bioinformatics Team at the University of Texas
• Open wikiBook Next Generation Sequencing (NGS)

There's also an excellent seminar series on iTunesU that covers a wide range of NGS topics - very appropriate for NGS newbies, grad students, etc. - sponsored by the Smithsonian Institution

Smithsonian Institution National Museum of Natural History - Next Gen Sequencing https://itunes.apple.com/us/itunes-u/next-gen-sequencing/id419187633?mt=10

There's also George Church's lectures on NGS and genomics at the MIT Open University https://itunes.apple.com/us/itunes-u/genomics-computational-biology/id341598226?mt=10

My be this not what you are looking for, but this might be helpful http://www.csc.fi/english/csc/courses/archive/ngs_workshop