Our new paper on the Cufflinks reference annotation based transcript (RABT) assembly method introduced in v1.0.0 has appeared in Bioinformatics. The paper describes how the RABT assembler builds upon a known reference annotation to better identify novel transcripts. You can try the RABT assembler in Cufflinks by using the -g option as explained in the manual.

Please cite this paper as well as the original Cufflinks paper if using the RABT assembler in your work.