NAR RNASEQR a RNA seq pipeline written in python

RNASEQR was written in Python 2.7 and runs on 64-bit Linux systems. It employs a Burrows–Wheeler transform (BWT)-based and a hash-based indexing algorithm. Briefly, there are three sequential processing steps: the first step is to align RNA-Seq sequences to a transcriptomic reference; the second step is to detect novel exons; the third step is to identify novel splice junctions using an anchor-and-align strategy.

http://m.nar.oxfordjournals.org/content/early/2011/12/22/nar.gkr1248.full