Back when Sanger sequencing was the most popular method, analyzing the sequence data was a simple task and only required relatively little background. Now, with the rapid and overwhelming development of next-generation sequencing, even learning about it seems like a daunting task. As a person still very much unfamiliar with the field, I feel lost in the amount of information that I need to digest: the assembly and alignment methods, the amount of available apps, the pipeline, the different platforms, etc -- I'm confused where I should start!
So my question would be: What is the most comprehensive resource to learn about next-generation sequencing data analysis? Preferably using SOLiD and/or Illumina (going from the most raw data to the final sequence).
I realize the answer might be very long-winded, but what I'm looking for is at least pointers so I can figure out what I need to know next on my own. I very much want to be able to analyze and interpret the data flood that is coming out of the field, but I'm pretty clueless right now. The things I know I learned from various, separate sources and sometimes it's hard to tie them together. So I this information would be a huge help for me (and I'm sure for other initiates alike :) ).
A little bit background: I'm familiar with UNIX (Linux), know a bit of Python and Java (if that helps). Currently I am doing a research project that involves building and assembling SOLiD and Illumina RNA-seq data to a reference genome sequenced using 454.