Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-microbiome-qiime2-workflow

Maintainer FreedomIntelligence · Last updated April 1, 2026

QIIME2 command-line workflow for 16S/ITS amplicon analysis. Alternative to DADA2/phyloseq R workflow with built-in provenance tracking. Use when preferring CLI over R, needing reproducible provenance, or working within QIIME2 ecosystem.

OpenClawNanoClawAnalysisReproductionbio-microbiome-qiime2-workflow🧬 bioinformatics (gptomics bio-* suite)bioinformatics — metagenomics & microbiomeqiime2

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-microbiome-qiime2-workflow

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

CLI: qiime dada2 denoise-paired, qiime diversity core-metrics-phylogenetic.
Run my amplicon analysis through QIIME2" → Process 16S/ITS amplicon data end-to-end using the QIIME2 CLI with built-in provenance tracking, from import through denoising, taxonomy, and diversity analysis. CLI: qiime dada2 denoise-paired, qiime diversity core-metrics-phylogenetic.
qiime tools import \ --type 'SampleData[PairedEndSequencesWithQuality]' \ --input-path manifest.tsv \ --output-path demux.qza \ --input-format PairedEndFastqManifestPhred33V2.

Source Doc

Excerpt From SKILL.md

View demultiplexed summary

qiime demux summarize
--i-data demux.qza
--o-visualization demux.qzv


## DADA2 denoising (creates ASV table + representative sequences)

qiime dada2 denoise-paired \
    --i-demultiplexed-seqs demux.qza \
    --p-trunc-len-f 240 \
    --p-trunc-len-r 160 \
    --p-trim-left-f 0 \
    --p-trim-left-r 0 \
    --p-max-ee-f 2 \
    --p-max-ee-r 2 \
    --p-n-threads 0 \
    --o-table table.qza \
    --o-representative-sequences rep-seqs.qza \
    --o-denoising-stats denoising-stats.qza

## View denoising stats

qiime metadata tabulate \
    --m-input-file denoising-stats.qza \
    --o-visualization denoising-stats.qzv