Can “gtdbtk identify” also output nucleotide sequences and not only protein sequences?
I use the flag “–write_single_copy_genes” and in the output folder are only aa-sequences.
Same goes for the “marker_genes” folder
Thanks for your help!
Hi,
GTDB-Tk works exclusively on protein sequences.
Cheers,
Donovan
Thank you for your quick response !!
Are there scripts publicly available that were used for extracting the marker gene DNA for the GTDB releases (as you know both dna and protein marker genes are reported for the species representatives)?
That would of great help - otherwise in the long run I might have to tweak GTDBtk to have prodigal output the nucleotide sequences and see how difficult it is to go from there as I am working with the gtdb nucleotide marker gene sequences.
If you have any further insight that might be helpful for me that would be very appreciated!!
Thanks again 
Hi,
We call genes de novo using Prodigal for GTDB and GTDB-Tk, but only produce genes in amino acid space.
Cheers,
Donovan