I just wanted to ask if you think it might be possible to include an option in the gc-assembler for assembling user defined functional classes? I.e. I would like to be able to align against a certain set of proteins that are not in any of Eggnog etc., and be able to assemble proteins belonging to that class from a metagenome.
Right now I would just pick an unused EGGNOG class and provide a synomyms file that map my protein references to that class, assemble contigs and relabel them as my original class, but this seems a bit ‘dirty’ and it would be nice to have that functionality for increased flexibility.
Let me know if you think that would be possible or is already in some cleaner way possible (e.g by adding custom classes to the internal eggnog.map of megan)!