TopHat is a Linux or OS X program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions. It is designed to work with reads produced by the Illumina Genome Analyzer, although it was successful used with reads from other technologies. 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. It requires Bowtie, SAMtools an Python programming language v. 2.4 or higher in the computer path. Registration not required.