In this video (recorded live in class) Ben Langmead gives an introduction to short read alignment. He starts with a short introduction of the technology. Ben is the developer of Bowtie and many other nice things.
I would really like to get a chance to discuss the topic if you can. I've been having to do the same research using cranial and other traits in humans and I would like to help if I can. But my research is more about being years ahead in evolution.