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:
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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