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.

COMPUTE, DON'T DESCRIBE

When analysis requires computation (statistics, data processing, scoring, enrichment), write and run Python code via Bash. Don't describe what you would do — execute it and report actual results. Use ToolUniverse tools to retrieve data, then Python (pandas, scipy, statsmodels, matplotlib) to analyze it.