Dear Gtdb team,
I am wonder where I can find the quality of all genomes in gtdb v202. It takes so long for me to run checkm for entire collection.
Many thanks,
Jianshu
Hi Jianshu,
CheckM completeness and contamination estimates are in the GTDB metadata files found at:
https://data.gtdb.ecogenomic.org/releases/release202/
A description of all provided files can be found in:
https://data.gtdb.ecogenomic.org/releases/release202/202.0/FILE_DESCRIPTIONS
You are after:
https://data.gtdb.ecogenomic.org/releases/release202/202.0/ar122_metadata_r202.tar.gz
https://data.gtdb.ecogenomic.org/releases/release202/202.0/bac120_metadata_r202.tar.gz
https://data.gtdb.ecogenomic.org/releases/release202/202.0/auxillary_files/metadata_field_desc.tsv
Cheers,
Donovan