| Tool name | TopHat |
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| URL | http://tophat.cbcb.umd.edu/index.html |
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| Important features | 1. It is a splice junction mapper which aligns RNA-Seq reads to large sized genomes using short read aligner bowtie.
2. It gives an output of splice junctions between exons from the mapping results. |
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| Citations | Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009 May 1;25(9):1105-11. Epub 2009 Mar 16. PubMed PMID:
19289445; PubMed Central PMCID: PMC2672628. |
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| Year of publication | 2009 |
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| Rank by usage frequency | 100 |
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| Comments | |
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| Function | RNA seq alignment |
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| Category | Free, Downloadable |
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| License | |
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| Status | Working |
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| Input file format | gzip or bzip2 compressed FASTA or FASTQ |
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| Output file format | |
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| Operating system | Linux/Unix 64bit
Mac X OS 64bit |
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| Operating language | C++ and Python |
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| Platform | Illumina/Solexa,
ABI SOLiD |
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| Maintained by | University of Maryland Center for Bioinformatics and Computational Biology and the University of California. |
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| Downloadable file format | |
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| Submission file format | |
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