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TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

Installed version

The currently installed version of TopHat is 2.1.1.

Using TopHat on the HPC cluster

If you want to use TopHat on the HPC Cluster, you will have to load its corresponding module first. You can do this with the command

module load TopHat/2.1.1


You can find the TopHat manual here.