We are big fans of using GTDB-Tk for our contig bins from Metabat etc. but would also really like to use it for our gene bins from programs such as MSPminer. Currently, we are using the suboptimal strategy of just providing the nucleotide sequences of our gene bins resulting in prodigal having to refind the genes and not having the necessary context such at Shine-Delgarno sequences and TATA-boxees. It would be great if we could just provide the genes and I tried to look at your code but didn’t really understand the structure well enough to see an easy way to provide genes instead of the built-in prodigal step. Any ideas?
Merry Christmas from Copenhagen!