Just to notice that in https://github.com/cboursnell/transfuse the parameter "--assembly" in the example command seems to be wrong. Instead it should be "--assemblies", shouldn't?
Yeah it should be
assemblies. Cheers for the spot. Will fix now.
How is transfuse working out for you?
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)
I've been doing some tests recently and putting some figures together.
This is from several assemblies done with soap varying the size of the kmer used. I aligned the contigs to the genome using blat and then plotted the query coverage on the y against the contigs in order on x
the 'm' line is the five other assemblies merged together with transfuse
the transrate score goes from
0.165 at the highest for the individual to 0.489 for the merged