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 is 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.

Cufflinks is provided under the OSI-approved Boost License


Differential analysis of gene regulation at transcript resolution with RNA-seq

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

Identification of novel transcripts in annotated genomes using RNA-Seq

Improving RNA-Seq expression estimates by correcting for fragment bias

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation