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Alternative name: TopHat2

Aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie. TopHat also analyzes the mapping results to identify splice junctions between exons. It can align reads of various lengths produced by the latest sequencing technologies, while allowing for variable-length indels with respect to the reference genome. The tool combines the ability to identify novel splice sites with direct mapping to known transcripts, producing sensitive and accurate alignments, even for highly repetitive genomes or in the presence of pseudogenes.

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2 user reviews

2 user reviews

Arup Ghosh's avatar image Arup Ghosh's country flag

Arup Ghosh

A popular tool for RNA-seq alignment but major disadvantages are slow and support discontinued after the launch of HISAT.

Claudia Armenise Quartz Bio's avatar image

Claudia Armenise Quartz Bio

Useful tool to map mRNA-seq reads, i.e. to align reads mapping onto multiple exons. Unfortunately, the support team is not very reactive to fix bugs.

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TopHat classification

TopHat specifications

Software type:
Restrictions to use:
Programming languages:
C++, Python
Bowtie, Bowtie-align, Bowtie-inspect, Bowtie-build, samtools
Command line interface
Operating system:
Unix/Linux, Mac OS
Computer skills:

TopHat distribution


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TopHat support



  • Cole Trapnell <>


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Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA; Department of Computer Science, University of Maryland, College Park, MD, USA; Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA, USA; Illumina Inc., San Diego, CA, USA

Funding source(s)

This work is supported in part by the National Human Genome Research Institute (NIH) under grants R01-HG006102 and R01-HG006677.

Link to literature

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