Site Map
News and updates
| New releases and related tools will be announced through the Bowtie mailing list. |
Getting Help
| Questions and comments about TopHat can be posted on the Tuxedo Tools Users Google Group. Please use tophat.cufflinks@gmail.com for private communications only. Please do not email technical questions to TopHat contributors directly. |
Releases
| version 2.1.1 | 2/23/2016 |
| Source code | |
| Linux x86_64 binary | |
| Mac OS X x86_64 binary |
Related Tools
- Cufflinks: Isoform assembly and quantitation for RNA-Seq
- Bowtie: Ultrafast short read alignment
- TopHat-Fusion: An algorithm for Discovery of Novel Fusion Transcripts
- CummeRbund: Visualization of RNA-Seq differential analysis
Publications
Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics doi:10.1093/bioinformatics/btp120
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.
Kim D and Salzberg SL. TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biology 2011, 12:R72
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. . Genome Biology 2013, 14:R36
Contributors
- Cole Trapnell
- Daehwan Kim
- Geo Pertea
- Harold Pimentel
- Ryan Kelley
- Lior Pachter
- Steven Salzberg
Links
Illumina has provided the RNA-Seq user community with a set of
genome sequence indexes (including Bowtie indexes) as well as GTF
transcript annotation files. These files can be used with TopHat and
Cufflinks to quickly perform expression analysis and gene discovery.
The annotation files are augmented with the tss_id and p_id
GTF attributes that Cufflinks needs to perform differential splicing,
CDS output, and promoter user analysis. We recommend that you download
your Bowtie indexes and annotation files from this page. More
information about Illumina's iGenomes project can be found
here.
| Organism | Data source | Version | Size | Last Modified |
|---|---|---|---|---|
| Homo sapiens | Ensembl | GRCh37 | 17297 MB | May 14 17:23 |
| NCBI | build36.3 | 15814 MB | May 14 19:36 | |
| build37.1 | 15850 MB | May 14 19:04 | ||
| build37.2 | 21450 MB | May 14 17:54 | ||
| UCSC | hg18 | 17349 MB | May 14 15:31 | |
| hg19 | 21058 MB | May 14 15:36 | ||
| Mus musculus | Ensembl | NCBIM37 | 14428 MB | May 14 22:13 |
| NCBI | build37.1 | 15260 MB | May 15 17:53 | |
| build37.2 | 15725 MB | May 14 22:52 | ||
| UCSC | mm9 | 14537 MB | May 14 21:12 | |
| mm10 | 14193 MB | Jun 14 11:29 | ||
| Rattus norvegicus | Ensembl | RGSC3.4 | 13725 MB | May 15 22:33 |
| NCBI | RGSC_v3.4 | 14234 MB | May 15 23:58 | |
| UCSC | rn4 | 13710 MB | May 15 22:32 | |
| Bos taurus | Ensembl | Btau_4.0 | 13315 MB | May 11 14:18 |
| UMD3.1 | 14042 MB | May 11 12:41 | ||
| NCBI | Btau_4.2 | 13357 MB | May 11 14:11 | |
| Btau_4.6.1 | 13448 MB | May 11 16:09 | ||
| UMD_3.1 | 13990 MB | May 11 16:08 | ||
| UCSC | bosTau4 | 13386 MB | May 11 12:36 | |
| Canis familiaris | Ensembl | BROADD2 | 13087 MB | May 11 18:00 |
| NCBI | build2.1 | 12847 MB | May 11 19:22 | |
| build3.1 | 12528 MB | May 11 19:30 | ||
| UCSC | canFam2 | 13138 MB | May 11 17:50 | |
| Gallus gallus | Ensembl | WASHUC2 | 5547 MB | May 14 12:30 |
| NCBI | build2.1 | 5592 MB | May 14 13:08 | |
| build3.1 | 5469 MB | May 14 13:18 | ||
| UCSC | galGal3 | 5546 MB | May 14 11:52 | |
| Drosophila melanogaster | Ensembl | BDGP5 | 669 MB | May 11 19:35 |
| BDGP5.25 | 692 MB | May 11 19:32 | ||
| NCBI | build4.1 | 701 MB | May 11 19:38 | |
| build5 | 701 MB | May 11 19:41 | ||
| build5.3 | 674 MB | May 11 19:40 | ||
| UCSC | dm3 | 763 MB | May 11 19:28 | |
| Arabidopsis thaliana | Ensembl | TAIR9 | 710 MB | May 11 10:47 |
| TAIR10 | 679 MB | May 11 10:46 | ||
| NCBI | build9.1 | 721 MB | May 11 10:51 | |
| TAIR10 | 658 MB | May 11 10:51 | ||
| Caenorhabditis elegans | Ensembl | WS210 | 597 MB | May 11 16:16 |
| WS220 | 560 MB | May 11 16:17 | ||
| NCBI | WS190 | 566 MB | May 11 16:21 | |
| WS195 | 554 MB | May 11 16:21 | ||
| UCSC | ce6 | 617 MB | May 11 16:13 | |
| ce10 | 552 MB | May 11 16:12 | ||
| Saccharomyces cerevisiae | Ensembl | EF2 | 74 MB | May 15 22:35 |
| EF3 | 72 MB | May 15 22:35 | ||
| EF4 | 71 MB | May 15 22:34 | ||
| NCBI | build2.1 | 70 MB | May 15 22:36 | |
| build3.1 | 70 MB | May 15 22:36 | ||
| UCSC | sacCer2 | 70 MB | May 15 22:34 | |
| sacCer3 | 70 MB | May 15 22:33 |