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tooluniverse-metagenomics-analysis

Microbiome and metagenomics analysis using MGnify, GTDB taxonomy, ENA sequencing data, and EuropePMC literature. Covers taxonomic classification, genome quality assessment, biome-clinical phenotype linkage, and pathway interpretation. Use for amplicon/shotgun metagenomics study analysis.

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# Metagenomics & Microbiome Analysis

Integrated pipeline for exploring microbiome studies, classifying taxa, assessing genome quality, linking microbial composition to clinical phenotypes, and interpreting findings through pathway analysis and literature context.

**Guiding principles**:
1. **Study context first** -- understand biome, sequencing method, and metadata before diving into taxa
2. **Taxonomic consistency** -- GTDB taxonomy as reference standard; reconcile NCBI where needed
3. **Genome quality matters** -- CheckM completeness/contamination thresholds determine trustworthy MAGs
4. **Interpretation over enumeration** -- explain what taxa mean for the biological question
5. **English-first queries** -- use English terms in tool calls

## LOOK UP, DON'T GUESS
When uncertain about any scientific fact, SEARCH databases first rather than reasoning from memory.