Processes paired-end 16S amplicon reads into QIIME 2 ASVs and taxonomy with retained artifact provenance. Checks paired FASTQ manifests, primer orientation diagnostics, predicted post-trimming overlap, sample IDs, runtime versions and read retention, and guides selection of compatible taxonomic classifiers.
Install
npx skills add K-Dense-AI/scientific-agent-skills --skill qiime2-ampliconnpx skills add K-Dense-AI/scientific-agent-skills --skill qiime2-amplicon -a claude-code -gnpx skills add K-Dense-AI/scientific-agent-skills --skill qiime2-amplicon -a codex -ggemini skills install https://github.com/K-Dense-AI/scientific-agent-skills.git --path skills/qiime2-amplicongh skill install K-Dense-AI/scientific-agent-skills qiime2-amplicongit clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills /tmp/K-Dense-AI__scientific-agent-skills
mkdir -p ~/.claude/skills ~/.agents/skills
cp -R /tmp/K-Dense-AI__scientific-agent-skills/skills/qiime2-amplicon ~/.claude/skills/qiime2-amplicon # Claude Code
cp -R /tmp/K-Dense-AI__scientific-agent-skills/skills/qiime2-amplicon ~/.agents/skills/qiime2-amplicon # Codex, Cursor, Gemini CLI, Copilot, OpenCode