Amplicon Processing (bioSkills)

A Claude Code skill that turns demultiplexed 16S rRNA or ITS amplicon FASTQ files into exact amplicon sequence variants (ASVs) using DADA2, handling the primer-removal and per-run error-modeling steps correctly.


Type	Claude Skill
Supplier	GPTomics bioSkills (community OSS, MIT)
Availability	GA — part of the bioSkills collection
Pricing	Free / OSS (MIT) — DADA2, cutadapt, QIIME2 and related tools are separately installed OSS
Capabilities	Read/Write — Claude runs the skill’s workflow locally (Bash/R), not as an MCP tool
Verified	works · 2026-07-27 — GPTomics/bioSkills resolves; clone + copy install path current
Security	cleared · 2026-07-27 — provenance matches GPTomics/bioSkills, MIT, maintained, no OSV advisories

How to install

bioSkills is not an npm package — skills are plain markdown/code read directly by the agent. Clone the repo, then either run the installer for the whole category or copy the single skill directory.

Claude Code — clone and install via the bundled script:
```
git clone https://github.com/GPTomics/bioSkills
cd bioSkills
./install-claude.sh --categories "microbiome"
```
The installer copies matching skills into ~/.claude/skills/ (default target). Use ./install-claude.sh --list to preview the skills first.
Claude Code / other agents — copy just this one skill:
```
cp -r bioSkills/microbiome/amplicon-processing ~/.claude/skills/
```
(run from inside your clone — the previous step left you in bioSkills/; otherwise replace bioSkills/ with the absolute path of your clone). Install DADA2 (R) / cutadapt / QIIME2 when prompted on first use.

What it does

Runs the denoising pipeline that converts raw amplicon reads into ASVs, enforcing the order-of-operations that DADA2 requires:

Primer removal — cutadapt with --discard-untrimmed (mandatory before quality filtering); ITSxpress for variable-length ITS spacer trimming.
Quality filtering — filterAndTrim() with expected-error and truncation thresholds.
Per-run error learning — learnErrors() fit to individual sequencing runs only (never pooled across runs).
Denoising — dada() against run-specific error models; Deblur available as a static-profile alternative for 16S.
Pair merging — mergePairs() with overlap validation.
Chimera + contaminant removal — DADA2 chimera detection and decontam for control-based contaminant identification.
QIIME2 available as a wrapper interface over DADA2/Deblur.

Primary use cases: 16S/ITS ASV inference, amplicon QC and denoising, feature-table generation for downstream taxonomy and diversity analysis.

Notes

Distributed as a SKILL.md (plus reference material) in the bioSkills collection — Claude executes the workflow locally rather than as an MCP server. The upstream skill front-matter name is bio-microbiome-amplicon-processing; if invoked as a namespaced plugin command it resolves under the bioSkills plugin, not as a bare /amplicon-processing. The output ASV table feeds taxonomy-assignment (classification) and the diversity/differential-abundance microbiome skills. Upstream directory: microbiome/amplicon-processing.

Sources

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