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.

TopHat is a collaborative effort between the Institute of Genetic Medicine at
Johns Hopkins University, the Department of Mathematics at the University of
California, Berkeley, and the Department of Stem Cell and Regenerative Biology
at Harvard University.

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
