Is it possible to get alignment of the submitted genomes that has the same length as genomes in GTDB ARB file? about gtdbtk HOT 2 CLOSED

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

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