Gtdb Tools

Configuration File: gtdb_tools.json Tool Type: Local Tools Count: 5

This page contains all tools defined in the gtdb_tools.json configuration file.

Available Tools

GTDB_get_genome (Type: GTDBTool)

Get comprehensive metadata for a specific genome by NCBI accession from GTDB. Returns nucleotide …

GTDB_get_genome tool specification

Tool Information:

  • Name: GTDB_get_genome

  • Type: GTDBTool

  • Description: Get comprehensive metadata for a specific genome by NCBI accession from GTDB. Returns nucleotide statistics (genome size, GC%, contig count, N50), gene-level metrics (completeness via CheckM/CheckM2, contamination, SSU/LSU counts, protein count, coding density), NCBI metadata (assembly level, BioProject, BioSample, isolation source, geographic coordinates), and taxonomic history across GTDB releases. Useful for evaluating genome quality, finding genome properties, and tracking taxonomic changes across GTDB versions.

Parameters:

  • operation (string) (required) Operation type (fixed: get_genome)

  • accession (string) (required) NCBI genome accession (e.g., ‘GCF_000005845.2’ for E. coli K-12, ‘GCF_000009045.1’ for B. subtilis)

Example Usage:

query = {
    "name": "GTDB_get_genome",
    "arguments": {
        "operation": "example_value",
        "accession": "example_value"
    }
}
result = tu.run(query)

GTDB_get_species (Type: GTDBTool)

Get detailed information about a GTDB species cluster, including all genomes assigned to that spe…

GTDB_get_species tool specification

Tool Information:

  • Name: GTDB_get_species

  • Type: GTDBTool

  • Description: Get detailed information about a GTDB species cluster, including all genomes assigned to that species. A GTDB species cluster groups genomes by average nucleotide identity (ANI). Returns the full list of genomes with their accessions, NCBI organism names, NCBI taxonomy, and whether they are the GTDB species representative or NCBI type material. Useful for exploring species diversity, finding representative genomes, and comparing GTDB vs NCBI classifications.

Parameters:

  • operation (string) (required) Operation type (fixed: get_species)

  • species (string) (required) Species name WITHOUT the s__ prefix (e.g., ‘Escherichia coli’, ‘Hydrogenothermus marinus’, ‘Bacillus subtilis’)

  • max_genomes (integer) (optional) Maximum number of genomes to return (default: 20). Species clusters can have thousands of genomes.

Example Usage:

query = {
    "name": "GTDB_get_species",
    "arguments": {
        "operation": "example_value",
        "species": "example_value"
    }
}
result = tu.run(query)

GTDB_get_taxon_info (Type: GTDBTool)

Get information about a GTDB taxon including its rank, total genome count, higher-rank lineage, a…

GTDB_get_taxon_info tool specification

Tool Information:

  • Name: GTDB_get_taxon_info

  • Type: GTDBTool

  • Description: Get information about a GTDB taxon including its rank, total genome count, higher-rank lineage, and release history. GTDB uses rank prefixes: d__ (domain), p__ (phylum), c__ (class), o__ (order), f__ (family), g__ (genus), s__ (species). For example, f__Lachnospiraceae returns its rank (Family), genome count, and lineage (Bacteria > Bacillota > Clostridia > Lachnospirales). Also returns the full lineage breakdown from domain to species. Useful for understanding where a taxon fits in the GTDB tree and how many genomes support it.

Parameters:

  • operation (string) (required) Operation type (fixed: get_taxon_info)

  • taxon (string) (required) GTDB taxon name with rank prefix (e.g., ‘f__Lachnospiraceae’, ‘d__Bacteria’, ‘g__Escherichia’, ‘s__Escherichia coli’). Use GTDB_search_taxon to find valid names.

Example Usage:

query = {
    "name": "GTDB_get_taxon_info",
    "arguments": {
        "operation": "example_value",
        "taxon": "example_value"
    }
}
result = tu.run(query)

GTDB_search_genomes (Type: GTDBTool)

Search for prokaryotic genomes in GTDB by organism name. Returns genome accessions with both NCBI…

GTDB_search_genomes tool specification

Tool Information:

  • Name: GTDB_search_genomes

  • Type: GTDBTool

  • Description: Search for prokaryotic genomes in GTDB by organism name. Returns genome accessions with both NCBI and GTDB taxonomy classifications, allowing comparison between the two taxonomic systems. Each result shows the genome accession (GCA/GCF), NCBI organism name, NCBI taxonomy, GTDB taxonomy, and whether the genome is a GTDB species representative. Supports pagination. Useful for finding genome accessions, exploring taxonomic reclassifications, and linking genomes to the GTDB taxonomy.

Parameters:

  • operation (string) (required) Operation type (fixed: search_genomes)

  • query (string) (required) Search query for organism name (e.g., ‘Escherichia’, ‘Staphylococcus aureus’, ‘Lactobacillus’)

  • page (integer) (optional) Page number for pagination (default: 1)

  • items_per_page (integer) (optional) Number of results per page (default: 10, max: 50)

Example Usage:

query = {
    "name": "GTDB_search_genomes",
    "arguments": {
        "operation": "example_value",
        "query": "example_value"
    }
}
result = tu.run(query)

GTDB_search_taxon (Type: GTDBTool)

Search the Genome Taxonomy Database (GTDB) for prokaryotic taxa by partial name. GTDB provides a …

GTDB_search_taxon tool specification

Tool Information:

  • Name: GTDB_search_taxon

  • Type: GTDBTool

  • Description: Search the Genome Taxonomy Database (GTDB) for prokaryotic taxa by partial name. GTDB provides a standardized genome-based taxonomy for Bacteria and Archaea, resolving polyphyletic groups in NCBI taxonomy. Returns matching taxon names with GTDB rank prefixes (d__=domain, p__=phylum, c__=class, o__=order, f__=family, g__=genus, s__=species). Search is case-insensitive and matches partial names. Use this for looking up standardized prokaryotic taxonomy names, finding correct GTDB identifiers, or exploring taxonomic groups like Lachnospiraceae, Enterobacteriaceae, or Clostridia.

Parameters:

  • operation (string) (required) Operation type (fixed: search_taxon)

  • query (string) (required) Partial taxon name to search for (e.g., ‘Lachnospiraceae’, ‘Escherichia’, ‘Bacillota’). Case-insensitive.

  • limit (integer) (optional) Maximum number of results per rank (default: 20, max: 100)

Example Usage:

query = {
    "name": "GTDB_search_taxon",
    "arguments": {
        "operation": "example_value",
        "query": "example_value"
    }
}
result = tu.run(query)