Individual skill
metagenomics
Metagenomic analysis — taxonomic profiling, assembly, binning, and functional annotation of microbiomes.
skills/metagenomics/SKILL.md
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## Overview
metagenomics covers shotgun sequencing of microbial communities: taxonomic profiling (who's
there), assembly and binning (recovering genomes), functional annotation (what they can do),
and the compositional statistics that microbiome data demands. It complements amplicon
(16S) approaches with strain-level resolution and functional insight — at higher cost and
complexity.
## When to use
- Study design: shotgun vs 16S, sequencing depth, controls (blanks, mocks).
- Taxonomic profiling: Kraken2, MetaPhlAn, and database biases.
- Assembly: MEGAHIT, metaSPAdes for complex communities.
- Binning: MetaBAT2, CONCOCT, DAS Tool → MAGs and quality assessment (CheckM).