TopHat (bioinformatics)

TopHat is an open source bioinformatics tool built to align RNA sequencing reads, the short cDNA fragments produced by shotgun transcriptome sequencing experiments, against mammalian sized reference genomes. It works in two stages: it first uses the Bowtie aligner to place the bulk of reads quickly against the genome, then processes the remaining unmapped reads to identify where they span exon-exon junctions produced by RNA splicing. Because it works out these splice junctions directly from the read data rather than relying on a supplied list of known junctions, TopHat can discover splice sites de novo, including junctions unique to a particular tissue or condition that were not previously catalogued. This made it a widely adopted step in RNA-seq analysis pipelines for building transcript models and quantifying gene expression from short read sequencing data.