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.

TopHat2 (the current release) is a collaborative effort between the Center for Computational Biology at Johns Hopkins University and the Genome Sciences Department at the University of Washington.

Please see http://ccb.jhu.edu/software/tophat for more information.

Note on compiling the package from source:

TopHat requires the Boost libraries (http://www.boost.org). Please see http://ccb.jhu.edu/software/tophat/tutorial.shtml#boost for documentation about building TopHat2 from source