Alternative splicing increases the functional complexity of a genome by generating multiple isoforms and potentially proteins from the same gene. Vast amounts of alternative splicing events are routinely detected by short read deep sequencing technologies but their functional interpretation is hampered by an uncertain transcript context. Emerging long-read sequencing technologies provide a more complete picture of full-length transcript sequences. We introduce SpliceHunter, a tool for the computational interpretation of long reads generated by for example Pacific Biosciences instruments. SpliceHunter defines and tracks isoforms and novel transcription units across time points, compares their splicing pattern to a reference annotation, and translates them into potential protein sequences.