Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-qiime2-amplicongit clone --depth 1 https://github.com/AlterLab-IEU/AlterLab-Academic-SkillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-qiime2-amplicon)<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-qiime2-amplicon"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-qiime2-amplicon/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-qiime2-amplicon"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-qiime2-amplicon.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector warn
SkillSpector: 1 finding, up to medium
These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →
- medium Output Handling · line 156 Output size or generation rate is not bounded. Unbounded output enables denial-of-service through resource exhaustion, log flooding, or context-window stuffing.Fix: Set explicit limits on output length, generation count, and rate. Use max_tokens and truncation to prevent unbounded output.
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00266 | $0.03661 |
| Opus 5 | $0.00133 | $0.01831 |
| Sonnet 5 | $0.00053 | $0.00732 |
| Haiku 4.5 | $0.00027 | $0.00366 |
Grade A, and why
alterlab-qiime2-amplicon scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 12d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 256 lines — stays where its author put it; the contents beside it link to each section on GitHub.
QIIME 2 Amplicon — 16S/ITS Microbiome Pipeline (FASTQ → Feature Table → Taxonomy → Diversity)
The command-line, workflow-runner entry point for marker-gene (amplicon) microbiome analysis. Given raw demultiplexed paired-end reads, it walks the canonical QIIME 2 order — import → primer trim → denoise → classify → diversity — and teaches the two things people get wrong most: trimming primers BEFORE DADA2, and the .qza/.qzv provenance model. It is the raw-data-to-result pipeline that hands a feature table off to in-memory analysis skills (see routing below).
Pinned to QIIME 2 2026.1 (the amplicon distribution). Forward-compat note: the
distribution is renamed qiime2 in 2026.4 — the env name and channel URL change, the
plugin commands below do not.
When to Use This Skill
Use this skill when the request involves running an amplicon / microbiome pipeline from sequencing reads:
- "Run a QIIME 2 16S pipeline on my paired-end reads."
- "I have ITS amplicon FASTQs — denoise with DADA2 and assign taxonomy."
- "Build a feature table / ASV table and classify against SILVA."
- "Pick truncation lengths from my quality plot and run core-metrics diversity."
- "How do I trim primers before DADA2 in QIIME 2?"
- "What's the right order of QIIME 2 commands?"
Does NOT Trigger — route these elsewhere
| The request is really about… | Route to |
|---|---|
| Alpha/beta diversity, UniFrac, PCoA ordination, PERMANOVA on an already-exported feature/distance table (in-memory, Python) | alterlab-scikit-bio |
| Building / manipulating a phylogenetic tree, tree visualization, or comparative phylogenetics outside QIIME 2 | alterlab-phylogenetics / alterlab-etetoolkit |
| Shotgun metagenomics taxonomic profiling, MAG assembly, functional genes (not marker-gene amplicons) | not in this skill — amplicon only; flag the gap |
| RNA-seq transcript quantification (salmon/kallisto), differential expression | alterlab-rnaseq-quant → alterlab-pydeseq2 |
| Variant calling FASTQ → VCF (germline/somatic) | alterlab-nf-core-sarek |
| Protein/nucleotide sequence similarity search (BLAST+/DIAMOND) | alterlab-blast |
| Spatial transcriptomics neighborhood/enrichment analysis | alterlab-squidpy-spatial |
| Quick one-off gene/sequence/database lookups | alterlab-gget |
| Reading/writing BAM/SAM/VCF, alignment file surgery | alterlab-pysam |
What ships with it
8 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 12d ago First seen · 256 lines · 266 tokens per session scan A 40e49d883f3e
alterlab-qiime2-amplicon is a skill published in the GitHub repository AlterLab-IEU/AlterLab-Academic-Skills (66 stars, last pushed 7d ago), licensed MIT. It adds 266 tokens to every session and 3,661 once invoked, about $0.0013 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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