Why to recalculate RED values?

Valentin_Berrios · August 5, 2021, 10:19pm

Hello I was tkaing a look into classify’s flag options and saw that it is possible to recalculate RED values , how does this affect on the classification of MAGs ?

Thanks for your time

donovan.parks · August 7, 2021, 5:32pm

Hi Valentin,

I am consulting with my colleagues, but I believe the short answer here is that this option causes RED values to be recalculated with the inclusion of your genomes. This is an experimental option as we haven’t fully explored the consequence of this. Given that this is likely to cause confusion, I think we will remove this option in the next GTDB-Tk release.

Cheers,
Donovan

donovan.parks · August 9, 2021, 2:21pm

Hi Valentin,

We will be removing this argument in the next GTDB-Tk release since we have not formally tested this approach.

Cheers,
Donovan