TopHat is a bioinformatic sequence analysis package tool for fast and high throughput alignment of shotgun transcriptomic cDNA sequencing reads (for example, RNA-Seq) using Bowtie first and then mapping to a reference genome to discover RNA splice sites de novo.
TopHat was originally developed in 2009 by Cole Trapnell, Lior Pachter and Steven Salzberg at the Center for Bioinformatics and Computational Biology at the University of Maryland, College Park. Trapnell later moved to Genome Sciences Department at the University of Washington. Currently TopHat is a collaborative effort between Cole Trapnell at the University of Washington and Daehwan Kim and Steven Salzberg in the Center for Computational Biology at Johns Hopkins University who together in 2013 also came up with TopHat2 which does accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.