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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