We have developed a tool SOAPsplice for genome-wide ab initio detection of splice junction sites from RNA-Seq, a method using new generation sequencing technologies to sequence the messenger RNA.
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install soapsplice
and update with:
conda update soapsplice
A Docker container is available at https://quay.io/repository/biocontainers/soapsplice.