There's an on-going thread at SEQanswers ("Hello - I use to think I was good with a computer") with tips on dealing with sequencing data. First, Jon_Keats posts some gems that he recently learned, namely that "my boss should have made me read and do the 'Unix and Perl for Biologist' tutorial years ago" and "BWA can align on my laptop ... cool ... next-gen/2nd gen alignment on a laptop and I [thought] I needed a super computer." Keats later posts a more technical fast-start guide for using Unix and Xcode as well as compiling applications.
HT: Nils Homer