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...
If you use python for NGS data anaysis this page is will very informative for you:
https://extras.csc.fi/biosciences/courses/ngs/htseq/HTSeq_tour.pdf
http://www-huber.embl.de/users/anders/HTSeq/doc/tour.html