- Unique identifier:
- Software type:
- Restrictions to use:
- Programming languages:
- C++, Python
- Bowtie, Bowtie-align, Bowtie-inspect, Bowtie-build, samtools
- Alternative name:
- Command line interface
- Operating system:
- Unix/Linux, Mac OS
- Computer skills:
- Documentation: http://ccb.jhu.edu/software/tophat/manual.shtml
- Cole Trapnell <>
No open topic.
(Kim et al., 2013)
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.
PMID: 23618408 DOI: 10.1186/gb-2013-14-4-r36
(Trapnell et al., 2009)
TopHat: discovering splice junctions with RNA-Seq.
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
This work is supported in part by the National Human Genome Research Institute (NIH) under grants R01-HG006102 and R01-HG006677.