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Welcome to the GTDB wiki! This wiki contains information for GTDB developers.

Updating to a new release of RefSeq/GenBank (Bacteria/Archaea):

• Sync with RefSeq/GenBank
• Update database metadata
• Updating GTDB species representatives
• Infer and decorate tree for new release
• Create SILVA SSU mapping file
• Check Integrity of GTDB
• Internal GTDB Release Notes

Other guides:

• Update GTDB taxonomy
• Generating data files for GTDB website
• Create GTDB SSU tree
• Update LTP Database
• Explicitly defining synonym species (e.g. Shigella spp. being synonyms of E. coli)
• Useful PostgresQL Commands

Running the GTDB tool:

• Taxonomy

Updating to a new release of RefSeq/GenBank (Fungal):

• Fungi - Sync with RefSeq/GenBank

Deprecated:

• Generate new exception lists