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TopHat is a fast splice junction mapper for RNA-Seq reads. It 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 among Daehwan Kim and Steven Salzberg in the Center for Computational Biology at Johns Hopkins University, and Cole Trapnell in the Genome Sciences Department at the University of Washington. TopHat was originally developed by Cole Trapnell at the Center for Bioinformatics and Computational Biology at the University of Maryland, College Park.


TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

TopHat: discovering splice junctions with RNA-Seq