TopHat specifications

Unique identifier:
OMICS_01257
Software type:
Application/Script
Restrictions to use:
None
Programming languages:
C++, Python
Version:
2.1.1
Requirements:
Bowtie, Bowtie-align, Bowtie-inspect, Bowtie-build, samtools
Wikipedia:
https://en.wikipedia.org/wiki/TopHat_(bioinformatics)
Alternative name:
TopHat2
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes

versioning

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No versioning.

TopHat distribution

download

TopHat support

Documentation

Maintainer

  • Cole Trapnell <>

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Credits

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Publications

Institution(s)

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.

User review

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2 user reviews

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2 user reviews

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

Arup Ghosh

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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

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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.