Cufflinks 0.7.0 released

  • 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