I can't believe it's been over a month since you packaged tranfuse (after my persistent requests)... I have disappeared into a code refactoring black hole- transferring my projects from the last 2 years into iPython notebooks - and am just now getting back to the assembly phase. I will be giving transfuse a go hopefully this month, and will see if merging cufflinks/SOAP/Trinity gives us significantly better assemblies (according to transrate as well as reproducibility between replicates)