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News and updates
| New releases and related tools will be announced through the mailing list |
Releases
| version 0.8.0 (BETA) | 2/5/2010 |
| Source code | |
| Linux x86_64 binary | |
| Mac OS X x86_64 binary |
Related Tools
Publications
Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. (manuscript under review)
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.
Contributors
- Cole Trapnell
- Geo Pertea
- Brian Williams
- Ali Mortazavi
- Gordon Kwan
- Jeltje van Baren
- Steven Salzberg
- Barbara Wold
- Lior Pachter
Links
0.8.0 release - 2/5/2010
We are happy to announce a major update to Cufflinks that introduces some powerful new features and includes a number of performance improvement and bug fixes. Highlights include:
- Cufflinks now includes a new tool, "Cuffdiff", which performs testing for differential expression, splicing, promoter use, and coding sequence output on two or more RNA-Seq samples. See the greatly expanded manual for details.
- Cuffcompare now reports a file containing the "union" of all transfrags in the files you give it as input, greatly simplifying downstream validatation of novel transcripts.
- Cufflinks' assembler has been overhauled and optimized, resulting in a speedup of 4-5 times over version 0.7.0, and a greatly reduced memory footprint. Phasing of splicing events has also been improved.
- Many bugfixes.
0.7.0 release - 9/26/2009
The first public release of Cufflinks is now available for download. Cufflinks is a program for the comparative assembly of transcripts and the estimation of their abundances in an RNA-Seq experiment. It runs on Linux and OS X. It also comes with a tool to track transcripts across multiple samples, for example in a time course of RNA-Seq.
Cufflinks takes as input a file of alignments in SAM format, and reports transfrags in GTF format. You can use TopHat to align your reads, as TopHat reports its alignments in SAM format.
This software is a work in progress - it is a beta release, and new features will continue to be added over the next couple of weeks. To suggest a feature or report a bug, please email Cole Trapnell