Alterlab Qiime2 Amplicon

AlterLab Creative Technologies Laboratory

Runs 16S/ITS amplicon (microbiome) analysis with the QIIME 2 distribution (2026.7; the "amplicon" distribution was renamed "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…

Install

npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-qiime2-amplicon

npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-qiime2-amplicon -a claude-code -g

npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-qiime2-amplicon -a codex -g

gemini skills install https://github.com/AlterLab-IEU/AlterLab-Academic-Skills.git --path skills/bioinformatics/alterlab-qiime2-amplicon

gh skill install AlterLab-IEU/AlterLab-Academic-Skills alterlab-qiime2-amplicon

git clone --depth 1 https://github.com/AlterLab-IEU/AlterLab-Academic-Skills /tmp/AlterLab-IEU__AlterLab-Academic-Skills
mkdir -p ~/.claude/skills ~/.agents/skills
cp -R /tmp/AlterLab-IEU__AlterLab-Academic-Skills/skills/bioinformatics/alterlab-qiime2-amplicon ~/.claude/skills/alterlab-qiime2-amplicon   # Claude Code
cp -R /tmp/AlterLab-IEU__AlterLab-Academic-Skills/skills/bioinformatics/alterlab-qiime2-amplicon ~/.agents/skills/alterlab-qiime2-amplicon   # Codex, Cursor, Gemini CLI, Copilot, OpenCode

Install

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