NMDTools

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)