ANGUS is a site built around the 2010 course on Analyzing Next-Generation Sequencing Data. It contains a number of detailed tutorials on mapping, assembly, mRNAseq, ChIP-seq, and resequencing analysis. Enjoy!
http://ged.msu.edu/angus/index.html
I found one R package SeqinR very handy in statistical computing of NGS data.
SeqinR 2.0-1: a contributed package to the project for statistical computing devoted to biological sequences retrieval and analysis
Link...