GTDB Wiki

Information for GTDB developers.

Update to a new RefSeq/GenBank release (Bacteria, Archaea, and Fungi)

1. Download NCBI metadata and genome assembly data
2. Generate GTDB metadata
3. Update database metadata
4. Updating GTDB species representatives
5. Infer and decorate tree for new release
6. Create SILVA SSU mapping file
7. Internal GTDB Release Notes

Other guides

• Data dictionary
• Update GTDB taxonomy
• Generating data files for GTDB website
• Create GTDB SSU tree
• Update LTP Database
• Explicitly defining synonym species — e.g. Shigella spp. as synonyms of E. coli
• Useful PostgreSQL Commands

Running the GTDB tool

• Taxonomy

Deprecated

• Generate new exception lists