ANDES. This is a library and a set of applications that can be used to analyze the results of deep sequencing results. (See Li et al.: ANDES: Statistical tools for the ANalyses of DEep Sequencing. BMC Research Notes 2010 3:199.)
I found ANDES to be an useful bioinformatic pipeline. The one feature that I would like updated though, is for the output to produce UNIX/GNU friendly filenames i.e. replace "|" characters with underscores.