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.

WWW: http://cole-trapnell-lab.github.io/cufflinks/