Comments (2)
Hello,
There is currently no options to change the trimming in GTDB-Tk itself.
However one solution would be to replace the masks used by GTDB-Tk by the ones used for GTDB ( available through http://gtdb.ecogenomic.org/downloads ) by pointing the config.py file to those new masks.
Cheers,
Pierre
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Hi,
Your solution seems to work nicely.
I tested with one of my genomes. When I changed the maks file, GTDBTk stopped during pplacer step. But, I could get the alignment of my genome with the same length as genomes in the ARB file in the output directory. I tried inserting this genome into the ARB tree, and the genome was successfully inserted into a position that is consistent with both GTDBTk classificaiton and my prior knowledge.
Thank you very much for your help.
Ilnam
from gtdbtk.
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