alterlab-qiime2-amplicon
From the author
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 diversity core-metrics-phylogenetic — teaching the .qza/.qzv artifact-and-provenance model and the 2026.1 feature-table summarize change (the former summarize_plus). Use when the request mentions QIIME2, QIIME 2, qiime, 16S, 18S, ITS, amplicon, microbiome, ASV, DADA2 denoising, feature table, taxonomic classification, or core-metrics diversity. For downstream alpha/beta diversity, PCoA, and PERMANOVA on the exported feature table prefer alterlab-scikit-bio; this is conda-only (no pip install). Part of the AlterLab Academic Skills suite.
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npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-qiime2-amplicon -a claude-code
Installs to .claude/skills/alterlab-qiime2-amplicon/ · Each command fetches the skill straight from GitHub with the open skills CLI.
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