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Application data

Created by Cole Trapnell, Daehwan Kim, Lior Pachter, Steven Salzberg
Biological application domain(s) RNA-Seq alignment
Principal bioinformatics method(s) Sequence alignment, mapping
Technology Illumina, SOLiD, 454
Created at University of Maryland, Center for Bioinformatics and Computational Biology, University of California, Berkeley, Department of Mathematics

Johns Hopkins University, Center for Computational Biology

Maintained? Yes
Input format(s) FASTA, FASTQ
Output format(s) SAM, BED, WIG
Programming language(s) C++
Licence Boost
Operating system(s) Linux, Unix
Contact: [email protected]

Summary: TopHat is a fast splice junction mapper for RNA-Seq reads.

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.

See also: BOWTIE.

Version 2.0.9 was released in June 2013. A paper describing the numerous improvements in TopHat2 was published in Genome Biology in April 2013. Frequent updates are provided on the TopHat webpage,

Color Space

Latest versions of TopHat support SOLiD color space reads.



  1. Trapnell C, Pachter L, Salzberg SL. 2009. Bioinformatics
  2. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. 2013. Genome Biology

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