Using GTDB-Tk with gene binning tools

GTDB-Tk
1

Hi folks!

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!
Gisle Vestergaard

2

Hi Gisle,

Thanks for the kind words. I’ve flagged this as a feature to include in the next GTDB-Tk release. Unfortunately, this likely won’t happen until 2021 given upcoming holidays.

I don’t imagine the GTDB-Tk results will differ when providing your own genes as Prodigal is fairly good and certainly works for the “standard” genes used by GTDB-Tk to infer the position of MAGs in a reference tree. That said, I appreciate that it would be convenient to be able to provide GTDB-Tk with called proteins instead of having to needlessly run Prodigal.

Cheers,
Donovan

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