Splice graph prediction pipeline. SpliceGrapher predicts splice graphs using information from gene models, EST alignments and RNA-Seq data. RNA-Seq exonic alignments may be performed using any popular short-read alignment tool. RNA-Seq spliced alignments may be performed using a conventional short-read mapping tool with a database of splice junctions predicted by SpliceGrapher, or they may be performed using short-read spliced-alignment programs such as TopHat, followed by filtering using SpliceGrapher's database of predicted splice sites. SpliceGrapher incorporates all of this information to produce a comprehensive splice graph prediction.