|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
|Input format(s)||FASTA, FASTQ|
|Output format(s)||SAM, BED, WIG|
|Operating system(s)||Linux, Unix|
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, http://ccb.jhu.edu/software/tophat.
Latest versions of TopHat support SOLiD color space reads.
- Trapnell C, Pachter L, Salzberg SL. 2009. Bioinformatics
- Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. 2013. Genome Biology
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