fast splice junction mapper for RNA-Seq reads

 TopHat 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 University of Maryland
 Center for Bioinformatics and Computational Biology and the
 University of California, Berkeley Departments of Mathematics and
 Molecular and Cell Biology.