TopHat
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Application data |
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| Created by | Cole Trapnell, Daehwan Kim, Lior Pachter, Steven Salzberg |
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| Biological application domain(s) | RNA-Seq Alignment |
| Principal bioinformatics method(s) | 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: | tophat.cufflinks@gmail.com |
Summary: TopHat is a fast splice junction mapper for RNA-Seq reads.
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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.
Color Space
Latest versions of TopHat support SOLiD color space reads.
Links
References
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| Web Search | Wiki Sites | Scientific |
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