Mgnify Expanded Tools

Configuration File: mgnify_expanded_tools.json Tool Type: Local Tools Count: 4

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

Available Tools

MGnify_get_genome (Type: MGnifyExpandedTool)

Get detailed genome information from the MGnify genome catalog. Returns assembly quality metrics …

MGnify_get_genome tool specification

Tool Information:

  • Name: MGnify_get_genome

  • Type: MGnifyExpandedTool

  • Description: Get detailed genome information from the MGnify genome catalog. Returns assembly quality metrics (completeness, contamination, N50), taxonomy, geographic origin, rRNA counts, protein count, pangenome statistics, and cross-references to ENA. Example: MGYG000000001 returns a high-quality Firmicutes isolate genome with 98.6% completeness.

Parameters:

  • genome_id (string) (required) MGnify genome accession. Examples: ‘MGYG000000001’, ‘MGYG000535630’.

Example Usage:

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

MGnify_get_study_detail (Type: MGnifyExpandedTool)

Get detailed information about a specific MGnify metagenomics study. Returns study name, abstract…

MGnify_get_study_detail tool specification

Tool Information:

  • Name: MGnify_get_study_detail

  • Type: MGnifyExpandedTool

  • Description: Get detailed information about a specific MGnify metagenomics study. Returns study name, abstract, associated BioProject, centre, biomes, and counts of analyses/downloads. Complementary to MGnify_search_studies which lists studies. Example: MGYS00002008 is a Tara Oceans marine metagenomics study.

Parameters:

  • study_accession (string) (required) MGnify study accession. Examples: ‘MGYS00002008’, ‘MGYS00005292’.

Example Usage:

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

MGnify_list_biomes (Type: MGnifyExpandedTool)

Browse the MGnify biome hierarchy. Returns biome identifiers, names, and sample counts. Biomes ra…

MGnify_list_biomes tool specification

Tool Information:

  • Name: MGnify_list_biomes

  • Type: MGnifyExpandedTool

  • Description: Browse the MGnify biome hierarchy. Returns biome identifiers, names, and sample counts. Biomes range from engineered environments (bioreactors) to natural habitats (ocean, soil, host-associated). Useful for discovering what metagenomic data is available for specific environments.

Parameters:

  • depth (integer) (optional) Hierarchy depth to filter by (1=root, 2=second level, etc.).

  • page (integer) (optional) Page number (default 1).

  • page_size (integer) (optional) Results per page (default 25, max 100).

Example Usage:

query = {
    "name": "MGnify_list_biomes",
    "arguments": {
    }
}
result = tu.run(query)

MGnify_search_genomes (Type: MGnifyExpandedTool)

Search the MGnify genome catalog for metagenome-assembled genomes (MAGs) and isolate genomes. Fil…

MGnify_search_genomes tool specification

Tool Information:

  • Name: MGnify_search_genomes

  • Type: MGnifyExpandedTool

  • Description: Search the MGnify genome catalog for metagenome-assembled genomes (MAGs) and isolate genomes. Filter by taxonomy lineage or genome type. Returns quality metrics, taxonomy, and protein counts. Useful for finding reference genomes from specific microbial lineages.

Parameters:

  • taxonomy (string) (optional) Taxonomy lineage filter. Examples: ‘Firmicutes’, ‘Bacteroidetes’, ‘Proteobacteria’.

  • genome_type (string) (optional) Filter by genome source type. Options: ‘Isolate’, ‘MAG’.

  • page (integer) (optional) Page number (default 1).

  • page_size (integer) (optional) Results per page (default 25, max 100).

Example Usage:

query = {
    "name": "MGnify_search_genomes",
    "arguments": {
    }
}
result = tu.run(query)