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.

See http://tophat.cbcb.umd.edu for more information.

Notes on compiling the package from source:
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TopHat requires the Samtools package (http://samtools.sourceforge.net/) 
in order to generate and handle the compressed, binary alignment files (BAM).
The --with-bam=<bam_prefix> option of the configure script expects the
following subdirectories and files:

<bam_prefix>/include/bam/*.h (all the header files from Samtools)
<bam_prefix>/lib/libbam.a (obtained by compiling Samtools)

At the time of this writing the Samtools package does not have an
install routine the user will have to explicitly create the above 
directory structure (./include/bam/ and ./lib) and copy the required 
Samtools files as indicated (the header files and libbam.a)