We are happy to announce a major update to Cufflinks that introduces some powerful new features and includes a number of performance improvement and bug fixes. Highlights include:

• Cufflinks now includes a new tool, “Cuffdiff”, which performs testing for differential expression, splicing, promoter use, and coding sequence output on two or more RNA-Seq samples. See the greatly expanded manual for details.
• Cuffcompare now reports a file containing the “union” of all transfrags in the files you give it as input, greatly simplifying downstream validatation of novel transcripts.
• Cufflinks’ assembler has been overhauled and optimized, resulting in a speedup of 4-5 times over version 0.7.0, and a greatly reduced memory footprint. Phasing of splicing events has also been improved.
• Many bugfixes.