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