Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.
Cufflinks was originally developed as part of a collaborative effort between the Laboratory for Mathematical and Computational Biology, led by Lior Pachter at UC Berkeley, Steven Salzberg’s computational genomics group at the Institute of Genetic Medicine at Johns Hopkins University, and Barbara Wold’s lab at Caltech. The project is now maintained by Cole Trapnell’s lab at the University of Washington.
Cufflinks is provided under the OSI-approved Boost License
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Cufflinks has moved to GitHub Cufflinks 2.2.1 released Cufflinks 2.2.0 released Cufflinks 2.1.1 released TransDecoder - calling novel ORFs in RNA-Seq assemblies New google group for TopHat, Cufflinks, and CummeRbund users Cufflinks 2.1.0 released Cuffdiff 2 manuscript published at Nature Biotechnology Cufflinks 2.0.2 released Cufflinks 2.0.1 released Cufflinks 2.0.0 released Tophat and Cufflinks protocol published at Nature Protocols Cufflinks 1.3.0 released Cufflinks 1.2.0 released CummeRbund released Cufflinks 1.1.0 released iGenomes index and annotation packages available for download Cufflinks RABT assembly paper published Cufflinks 1.3.0 released Cufflinks 1.0.2 released Cufflinks 1.0.1 released Cufflinks Bias Correction paper published Cufflinks 0.99.0 released Cufflinks 0.9.3 released Cufflinks 0.9.2 released Cufflinks 0.9.2 released Cufflinks 0.9.1 released Cufflinks 0.9.0 released Cufflinks 0.8.3 released Cufflinks 0.8.2 released Cufflinks 0.8.1 released Cufflinks 0.8.1 released Cufflinks 0.7.0 released