Add external assemblies to OrthFuse?

[santiagorevale]

Hi Mathew,

I would like to be able to provide to the pipeline some additional transcriptome assemblies to be incorporated into the assembly merging step (OrthoFuse). Is that possible? I seem to recall having read somewhere that OrthFuse was created in such a way it could take additional assemblies. If this is so, how can I do it? If ORP cannot be setup to run this way, would it be possible to run everything from OrthoFuser onwards providing the additional assemblies? Any other recommendation?

The reason why I would like to be able to do this is because I'm trying to build a comprehensive transcriptome for a fly specie, and I have several sets of RNAseq data from different tissues/states/individuals/generations/lines. I also have a somewhat close reference genome I could use. So my idea based on some of your previous comments (on GitHub) would be to assemble each dataset individually, both de novo and reference guided, and then merge them as instructed in your pipeline (OrthoFurse, Transrate, Detonate, etc.). What do you think?

Thank you very much in advance for anything you could help me with.

Cheers,
Santiago