R-SAP (RNA-Seq analysis pipeline)

R-SAP is a user-friendly and fully automated bioinformatics pipeline that analyzes and quantitates high-throughput RNA-Seq datasets. R-SAP accurately characterizes various classes of transcripts resulted from aberrant splicing and chimeric transcripts. Expression level estimates are reported as RPKM (reads per kilobase of exon model per million mapped reads) values.

Download (from Sourceforge):
version 1.1: r-sap-v1.1   README    release notes
version 1.0: r-sap-v1.0   README

Contact:
Please report bugs and send questions/suggestions to: Vinay Mittal ( vinaykmittal@gatech.edu )

Reference:
Mittal VK, McDonald JF. 2012. R-SAP: a multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data. Nucleic Acid Reseaech. Jan. 28; Pubmed