This page lists the tools for the analysis pipeline specifically developed for the investigation of alternative splicing in the context of Nonsense Mediated Decay
Following tools are used in the NMD analysis pipeline:
- PALMapper is used for fast and accurate alignment of RNA-Seq read data to the resepctive reference genome
- RNAgeeq is a python toolbox for filtering and optimizing RNA-Seq read alignment data (used for multimapper correction)
- SPLADDER is a program, currently written in Matlab/Octave code, to augment existing annotation information on a splicing graph basis. It is further used to identify alternative splicing events within this splicing graph.
- GBrowse for visualization.
- scripts implemented in Matlab, bash and Python (available by the authors upon request)