Generate Ribosomal Metadata - Ecogenomics/GTDBNCBI GitHub Wiki
Identify, extract, and taxonomically classify 16S, 23S, and 5S rRNA genes in genomes against SILVA
- check if a new version of SILVA has been released (see Update Silva)
- need to run for 16S, 23S, and 5S rRNA genes
Current silva version: 138.2
Example:
> module load hmmer blast (optional)
> gtdb_migration_tk rna_silva -g /srv/db/gtdb/genomes/ncbi/release<release#>/genome_dirs.tsv -d /srv/db/gtdb/metadata/release<release#>/representatives/sp_cluster_update/gtdb_r232_domain_report.tsv -v 138.2 -p /srv/db/silva -r ssu -l ./logs/rna_silva_138.2_ssu.log -c 96
Identifies, extracts, and taxonomically classifies 16S rRNA genes in genomes against the Living Tree Project (LTP)
- check if a new version of LTP has been released
- need to run for 16S
Current LTP version: 10_2024
Current SSU version: 138.2
Example:
> gtdb_migration_tk rna_ltp -g /srv/db/gtdb/genomes/ncbi/release<release#>/genome_dirs.tsv -d /srv/db/gtdb/metadata/release<release#>/representatives/sp_cluster_update/gtdb_r232_domain_report.tsv --ltp_version 10_2024 --silva_version 138.2 -p /srv/db/silva/ltp/ -l ./logs/rna_ltp.log -c 96