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alterlab-qiime2-amplicon

82 / 100 · Low risk

Fine to try.

By stanfish06/skillquarium (GitHub) · research · 12 stars · scanned at commit ced6c96

Runs 16S/ITS amplicon (microbiome) analysis with the QIIME 2 amplicon distribution (2026.1; renamed to "qiime2" in 2026.4) in the correct order: manifest import, cutadapt trim-paired primer removal BEFORE dada2 denoise-paired (trunc-len chosen from the demux quality .qzv), feature-classifier classify-sklearn against a version-matched SILVA 138 or Greengenes2 classifier, and diversity core-metrics-phylogenetic — teaching the .qza/.qzv artifact-and-provenance model and the 2026.1 feature-table su…

Works with any agent that supports SKILL.md skills.

What this skill can do

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'alterlab-qiime2-amplicon' ] || [ -L ~/.agents/skills/'alterlab-qiime2-amplicon' ]; then echo 'A skill folder named alterlab-qiime2-amplicon already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/stanfish06/skillquarium' "$d" && git -C "$d" checkout --quiet 'ced6c96bd67acccbf0280a5071e59a523c118c66' -- 'skills/alterlab-qiime2-amplicon' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/alterlab-qiime2-amplicon' ~/.agents/skills/'alterlab-qiime2-amplicon' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'alterlab-qiime2-amplicon' ~/.claude/skills/'alterlab-qiime2-amplicon' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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