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
/plugin marketplace add PKU-EMBL/Metagenomics-Skills
/plugin install metagenomics@metagenomics-skills
git clone https://github.com/PKU-EMBL/Metagenomics-Skills.git
cd Metagenomics-Skills
./scripts/install-platforms.sh --user allskills/<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
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 / …
See CONTRIBUTING.md. New skills go under skills/<name>/
with upstream links and an “Analytical thinking” section.
MIT
Primary literature (Nature-style). Full numbered list: docs/references.md.
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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
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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
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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
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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
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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
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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
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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
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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.