bio-microbiome-qiime2-workflow
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.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-microbiome-qiime2-workflow --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: DADA2 1.30+, MAFFT 7.520+, QIIME2 2024.2+, phyloseq 1.46+, scanpy 1.10+, scikit-learn 1.4+ Before using code patterns, verify installed versions match. If versions differ: - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # QIIME2 Amplicon Workflow **"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` ## Import Data ```bash # Import paired-end FASTQ with manifest qiime tools import \ --type 'SampleData[PairedEndSequencesWithQuality]' \ --input-path manifest.tsv \ --output-path demux.qza \ --input-format PairedEndFastqManifestPhred33V2 # View demultiplexed summary qiime demux summarize \ --i-data demux.qza \ --o-visualization demux.qzv ``` ## Denoise with DADA2 ```bash # DADA2 denoising (creates ASV table + representative se
- Version Compatibility
- Import Data
- Denoise with DADA2
- Alternative: Deblur Denoising
- Taxonomy Assignment
- Phylogenetic Tree
- Diversity Analysis
- Differential Abundance (ANCOM)
- Export to R/Python
- Manifest File Format
- Metadata File Format
- Related Skills
Import paired-end FASTQ with manifest qiime tools import \ View demultiplexed summary qiime demux summarize \ DADA2 denoising (creates ASV table + representative sequences) qiime dada2 denoise-paired \ View denoising stats qiime metadata tabulate \ Quality filter first qiime quality-filter q-score \
What does the bio-microbiome-qiime2-workflow skill do?
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.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-microbiome-qiime2-workflow --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.