bio-workflows-microbiome-pipeline
End-to-end 16S amplicon workflow from FASTQ reads to differential abundance. Orchestrates DADA2 ASV inference, taxonomy assignment, diversity analysis, and compositional testing with ALDEx2. Use when processing 16S/ITS amplicon data.
npx skills add BioTender-max/awesome-bio-agent-skills --skill microbiome-pipeline --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+, ggplot2 3.5+, phyloseq 1.46+, scanpy 1.10+, vegan 2.6+ Before using code patterns, verify installed versions match. If versions differ: - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Microbiome Pipeline **"Run end-to-end 16S microbiome analysis from FASTQ"** → Orchestrate DADA2 denoising, taxonomy assignment, alpha/beta diversity (phyloseq), differential abundance (ALDEx2/ANCOM-BC2), and functional prediction (PICRUSt2). ## Pipeline Overview ``` Paired-End FASTQ (16S V4) │ ▼ ┌──────────────────────────────────────────────────┐ │ microbiome-pipeline │ ├──────────────────────────────────────────────────┤ │ 1. Quality Filtering (DADA2 filterAndTrim) │ │ 2. Error Learning & Denoising │ │ 3. Merge Pairs & Remove Chimeras │ │ 4. Taxonomy Assignment (SILVA) │ │ 5. Create phyloseq Object │ │ 6. Alpha/Beta Diversity │ │ 7. Differential Abundance (ALDEx2) │ │ 8. Visualization & Export │ └──────────────────────────────────────────────────┘
- Version Compatibility
- Pipeline Overview
- Complete R Workflow
- QC Checkpoints
- Output Files
- Workflow Variants
- ITS Fungal Workflow
- Different 16S Regions
- GTDB Taxonomy
- Related Skills
What does the bio-workflows-microbiome-pipeline skill do?
End-to-end 16S amplicon workflow from FASTQ reads to differential abundance. Orchestrates DADA2 ASV inference, taxonomy assignment, diversity analysis, and compositional testing with ALDEx2. Use when processing 16S/ITS amplicon data.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill microbiome-pipeline --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 BioTender-max/awesome-bio-agent-skills, a repository with 135 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.