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.

Reference:
Ali Mortazavi, Brian A Williams, Kenneth McCue, Lorian Schaeffer and
Barbara Wold, "Mapping and quantifying mammalian transcriptomes by
RNA-Seq", Nature Methods, volume 5, 621 - 628 (2008)
