PASTA for splice-junction detection in RNA-Seq data

PASTA (Patterned Alignment of Spliced Transcripts Analysis) – is a complete pipeline for the analysis of alternative splicing using RNA-Sequencing data. The first component of the pipeline, described in the rest of this page, implements a novel splice junction detection algorithm based on patterned subsequence alignments and a detailed, species-specific model of intronic context. The method is highly sensitive, and is able to reliably detect splice junctions even at low sequencing depths.
The program is highly configurable and easy to use. It is distributed as a command-line tool designed for inclusion in automated RNA-Seq analysis pipelines in a GNU/Linux environment.

AVAILABILITY:  PASTA was developed by the Riva Bioinformatics lab at the University of Florida, and can be downloaded from Common Lisp source code is available upon request.