Identifies splice junctions. SplitSeek allows de novo prediction of splice junctions in short-read RNA-seq data. The software consists of two programs that are executed sequentially. It can detect novel splice events and be used as a way to extend known gene models. The results can be directly uploaded to the UCSC genome browser and used as input to the BEDTools software suite, which enables user to visualize and analyze the predicted events in a genomic context.