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Metagenomics Skills

Agent Skills for shotgun metagenomics, organized by scientific stage:

QC → assembly → mapping → binning → taxonomy → function → microbial mining → research analysis

One skill per core tool (mappers, assemblers, binners, profilers, miners such as antiSMASH / geNomad / DRAM, …) plus databases, language-model hubs, homology / phylogenomics routing, and paper-facing stats/figures (research-analysis).

Getting started · Skills · Pipeline · Public databases · References · Platforms

Install

Claude Code

/plugin marketplace add PKU-EMBL/Metagenomics-Skills
/plugin install metagenomics@metagenomics-skills

Codex / Cursor / Kimi / Grok

git clone https://github.com/PKU-EMBL/Metagenomics-Skills.git
cd Metagenomics-Skills
./scripts/install-platforms.sh --user all

→ docs/multi-platform.md

Layout

skills/<tool>/SKILL.md     # per-software / per-database + analytical thinking
skills/<tool>/references/  # optional deep detail inside that skill only
docs/                      # stage catalogs and pipelines
.claude-plugin/ .codex-plugin/ .cursor-plugin/
scripts/install-platforms.sh

Quick start

Full genome-resolved path

study-design → QC (± multiqc) → assembly → mapping → binning (basalt recommended) → (± anvio / deepurify) → taxonomy / function → research-analysis (microeco / maaslin2 / …)

Community composition only (no assembly)

QC → taxonomy (metaphlan, singlem, or kraken2) → research-analysis

Research stats & figures

research-analysis → multiqc / microeco / phyloseq / visualization / maaslin2 / ancombc / lefse / stamp / sparcc / spieceasi

Workflow managers

nextflow (± nf-core) · snakemake

Genome-resolved + interactive polish

Auto-bins → anvio refine → checkm2 / gunc / mag-qc → gtdbtk

Viral / plasmid / MGE mining

Contigs → genomad / virsorter2 → checkv → vcontact · mobileog / isescan / integronfinder / mob-suite · plasmids: plasmaag · isolates: cge-finders (staramr / abricate / plasmidfinder → pmlst / mlst)

Microbial mining (BGCs / AMR / element cycling / DOM / defense / QS)

After MAGs: microbial-mining → antismash / rgi / cge-finders / element-cycling / dom-biosurfactant / dram / defensefinder / padloc / qsap / …

Homology search (Steinegger/Söding · vector DB · compressed genomes)

homology-search → mmseqs2 / hh-suite / foldseek / foldmason / plass / petasearch / erast / phylign / …

Phylogenomics / trees

phylogenomics → gtdbtk / phylophlan / unicore / iqtree / fasttree / lucaphylo

Genome language models

genome-language-model → omg / nucleotide-transformer (NTv3) / dnabert2 / caduceus / evo2

Protein language models

protein-language-model → esm / esmc / saprot / prostt5 / plmsearch / deepblast

AI / LMs & structure search (Foldseek · PLMs)

metagenomics-llm → genome-language-model / protein-language-model / foldseek / spacedust / …

Contributing

See CONTRIBUTING.md. New skills go under skills/<name>/ with upstream links and an “Analytical thinking” section.

License

MIT

References

Primary literature (Nature-style). Full numbered list: docs/references.md.

  1. Qiu, Z. et al. BASALT refines binning from metagenomic data and increases resolution of genome-resolved metagenomic analysis. Nat. Commun. 15, 2179 (2024). https://doi.org/10.1038/s41467-024-46539-7

  2. Uritskiy, G. V., DiRuggiero, J. & Taylor, J. MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis. Microbiome 6, 158 (2018). https://doi.org/10.1186/s40168-018-0541-1

  3. Sieber, C. M. K. et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat. Microbiol. 3, 836–843 (2018). https://doi.org/10.1038/s41564-018-0171-1

  4. Blanco-Míguez, A. et al. Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nat. Biotechnol. 41, 1633–1644 (2023). https://doi.org/10.1038/s41587-023-01688-w

  5. Beghini, F. et al. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. eLife 10, e65088 (2021). https://doi.org/10.7554/eLife.65088

  6. Almeida, A. et al. A unified catalog of 204,938 reference genomes from the human gut microbiome. Nat. Biotechnol. 39, 105–114 (2021). https://doi.org/10.1038/s41587-020-0603-3

  7. Parks, D. H. et al. A complete domain-to-species taxonomy for Bacteria and Archaea. Nat. Biotechnol. 38, 1079–1086 (2020). https://doi.org/10.1038/s41587-020-0501-8

  8. Richardson, L. et al. MGnify: the microbiome sequence data analysis resource in 2023. Nucleic Acids Res. 51, D753–D759 (2023). https://doi.org/10.1093/nar/gkac1080

Software repositories and Agent Skills packaging links are listed in docs/references.md only as implementation pointers; cite the papers above (plus versions/releases) in manuscripts.