tophat: tophat (Splice junction mapper for RNA-Seq reads) tophat: tophat: TopHat is a fast splice junction mapper for RNA-Seq reads. It tophat: aligns RNA-Seq reads to mammalian-sized genomes using the ultra tophat: high-throughput short read aligner Bowtie, and then analyzes the tophat: mapping results to identify splice junctions between exons. tophat: tophat: Home: http://tophat.cbcb.umd.edu/ tophat: https://github.com/infphilo/tophat/ tophat: tophat: