Arriba is a command-line tool to detect gene fusions from RNA-Seq data based on the STAR aligner. In addition to fusions, it can detect exon duplications/inversions and truncations of genes (i.e., breakpoints in introns and intergenic regions). Arriba is the winner of the DREAM SMC-RNA Challenge.

BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.