Generate Ribosomal Metadata - Ecogenomics/GTDBNCBI GitHub Wiki

Classification against SILVA

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)
  • Run for 16S, 23S, and 5S rRNA genes

Current SILVA version: 138.2

Example:

module load hmmer/3.1b2 ncbi-blast/2.16.0 (optional)

gtdb_migration_tk rna_silva -g ../../genomes/ncbi/<release>/genome_dirs.tsv -d ../metadata/<prev_release>/representatives/sp_cluster_update/gtdb_r<prev_release>_domain_report.tsv -t ncbi/taxonomy/standardised_taxonomy/ncbi_r<release>_standardized.tsv -v 138.2 -p /srv/db/silva -r ssu -o rna_silva -c 96 -l ./logs/rna_silva_138.2_ssu-<server>.log

gtdb_migration_tk rna_silva -g ../../genomes/ncbi/<release>/genome_dirs.tsv -d ../metadata/<prev_release>/representatives/sp_cluster_update/gtdb_r<prev_release>_domain_report.tsv -t ncbi/taxonomy/standardised_taxonomy/ncbi_r<release>_standardized.tsv -v 138.2 -p /srv/db/silva -r lsu_23S -o rna_silva -c 96 -l ./logs/rna_silva_138.2_lsu_23S-<server>.log

gtdb_migration_tk rna_silva -g ../../genomes/ncbi/<release>/genome_dirs.tsv -d ../metadata/<prev_release>/representatives/sp_cluster_update/gtdb_r<prev_release>_domain_report.tsv -t ncbi/taxonomy/standardised_taxonomy/ncbi_r<release>_standardized.tsv -v 138.2 -p /srv/db/silva -r lsu_5S -o rna_silva -c 96 -l ./logs/rna_silva_138.2_lsu_5S-<server>.log

The rna_silva command is run on batches of genomes (default = 10,000) so it can be run across multiple servers and to allow restarting if required. Final results are stored in the rna_silva_<version> directory of each genome.

Classification against LTP

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
  • Reed to run for 16S

Current LTP version: 10_2024

Example:

gtdb_migration_tk rna_ltp -g ../../genomes/ncbi/<release>/genome_dirs.tsv --ltp_version 10_2024 --ssu_version 138.2 -p /srv/db/silva/ltp -o rna_ltp -c 96 -l ./logs/rna_ltp_138.2_ssu-page.log

The rna_ltp command is run on batches of genomes (default = 10,000) so it can be run across multiple servers and to allow restarting if required. Final results are stored in the rna_ltp_<version> directory of each genome.

Note: the rna_ltp step uses the 16S rRNA genes identified by the rna_silva step

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