HMMSplicer – for finding splice junctions in RNA-Seq data

The DeRisi lab is pleased to release HMMSplicer to the community. This open-source software package discovers splice junctions in RNA-Seq datasets without using gene models. HMMSplicer was benchmarked on publicly available A. thaliana, H. sapiens, and P. falciparum datasets and performed well in all cases. The software was found to perform especially well in compact genomes and on genes with low expression levels, alternative splice isoforms, or non-canonical splice junctions. In addition, HMMSplicer provides a score for every predicted junction allowing the user to set a threshold to tune false positive rates depending on the needs of the experiment. Information about the datasets tested, including the exact command parameters and the final results, is provided. HMMSplicer is implemented in Python and is freely available for all. The manuscript is currently under review.

The code and documentation can be found at: