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tooluniverse-metagenomics-analysis

Analyzes microbiome studies using MGnify, GTDB, ENA, and GMrepo databases.

1.7k|254|Updated Mar 3, 2025
Search Tags:#taxonomy#Analyze#kegg#metagenomics#gtdb#microbiome#mgnify
One-click install
npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-metagenomics-analysis
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: tooluniverse-metagenomics-analysis
Source: https://github.com/mims-harvard/ToolUniverse/tree/main/plugins/tooluniverse/skills/tooluniverse-metagenomics-analysis
Command: npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-metagenomics-analysis

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Metagenomics research requires querying many disconnected databases (MGnify, GTDB, ENA, GMrepo, KEGG) with different query syntaxes and taxonomic conventions, making it hard to move from a biological question to an evidence-graded interpretation.

Core Features & Use Cases

  • Study Discovery & Taxonomy: Find processed metagenomics studies in MGnify and ENA, then classify taxa against the GTDB reference standard with NCBI reconciliation.
  • Genome Quality & Function: Assess MAG quality with CheckM completeness/contamination tiers (MIMAG) and map functional annotations to KEGG pathways like SCFA production and LPS biosynthesis.
  • Clinical Linkage & Literature: Connect gut species to human phenotypes via GMrepo MeSH terms and grade evidence strength from PubMed/EuropePMC literature.
  • Use Case: Ask how gut microbiome composition relates to Crohn's disease, and receive a report covering relevant studies, GTDB-classified taxa, pathway-level functional interpretation, and evidence-graded clinical associations.

Quick Start

Analyze the gut microbiome's association with Crohn's disease using MGnify studies, GTDB taxonomy, and GMrepo phenotype data, then summarize the functional pathways and evidence strength.

Frequently Asked Questions about tooluniverse-metagenomics-analysis

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I analyze a metagenomics study with MGnify and GTDB?▼

Search MGnify for processed studies matching your biome or phenotype, then classify identified taxa against GTDB using GTDB_search_taxon. Note that GTDB naming differs from NCBI, so reconcile discrepancies before interpreting results.

What databases are used for microbiome-disease association analysis?▼

GMrepo links gut species to human health phenotypes using MeSH terms, while PubMed and EuropePMC provide published microbiome-disease studies. CTD adds chemical-microbiome-disease relationships for mechanistic context.

Why does GMrepo return zero results for my disease query?▼

GMrepo requires formal MeSH terms, so use "Crohn Disease" instead of "IBD" or "Colorectal Neoplasms" instead of "colorectal cancer". If species names fail, try querying with NCBI taxon IDs instead.

How is metagenome-assembled genome quality assessed?▼

Quality follows MIMAG tiers based on CheckM metrics: high quality requires at least 90% completeness and 5% or less contamination, medium requires 50% completeness and 10% contamination. Low-quality genomes are flagged but not excluded.

Can this skill analyze raw FASTQ sequencing files?▼

No, it queries processed databases rather than analyzing raw sequence data. ENA provides raw dataset metadata and accessions, but actual sequence processing must be done with external bioinformatics pipelines first.

What are the limitations of GTDB and GMrepo for taxonomy?▼

GTDB covers only Bacteria and Archaea with its own naming convention, so eukaryotic microbes are excluded. GMrepo is gut-only, making it unsuitable for skin, oral, or environmental microbiome phenotype associations.

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