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 was designed to work with reads produced by the Illumina Genome Analyzer, although users have been successful in using TopHat with reads from other technologies.TopHat can find splice junctions without a reference annotation. By first mapping RNA-Seq reads to the genome, TopHat identifies potential exons, since many RNA-Seq reads will contiguously align to the genome. Using this initial mapping information, TopHat builds a database of possible splice junctions and then maps the reads against these junctions to confirm them.

Version: 2.1.1 (G100) 2.0.12 (Marconi)

Availability: GALILEO100

Target: all

Official web site:

Related Commands:

module load profile/bioinf

module load tophat2

module show tophat2

Help and Documentation:

You can find documentation on the system, with the command 'module help tophat2

- The manual is on the web at the original home page (


CINECA consultants can be reached through the address:'''

contact =