A structured microbiome workflow for reproducible ecological analysis and interpretation.
4.1 System Path
Code
flowchart TD A[FASTQ Files] B[Quality Control] C[Denoising and ASV Inference] D[Taxonomy Assignment] E[Diversity Analysis] F[Community Structure] G[Differential Abundance] H[Ecological Interpretation] I[Quarto Reporting] A --> B B --> C C --> D D --> E E --> F F --> G G --> H H --> I style A fill:#dbeafe,stroke:#2563eb,stroke-width:2px,color:#0f172a style B fill:#e0f2fe,stroke:#0284c7,stroke-width:2px,color:#0f172a style C fill:#ecfeff,stroke:#0891b2,stroke-width:2px,color:#0f172a style D fill:#ede9fe,stroke:#7c3aed,stroke-width:2px,color:#0f172a style E fill:#f3e8ff,stroke:#9333ea,stroke-width:2px,color:#0f172a style F fill:#fae8ff,stroke:#c026d3,stroke-width:2px,color:#0f172a style G fill:#fef3c7,stroke:#d97706,stroke-width:2px,color:#0f172a style H fill:#ecfccb,stroke:#65a30d,stroke-width:2px,color:#0f172a style I fill:#f0fdf4,stroke:#16a34a,stroke-width:2px,color:#0f172a
flowchart TD
A[FASTQ Files]
B[Quality Control]
C[Denoising and ASV Inference]
D[Taxonomy Assignment]
E[Diversity Analysis]
F[Community Structure]
G[Differential Abundance]
H[Ecological Interpretation]
I[Quarto Reporting]
A --> B
B --> C
C --> D
D --> E
E --> F
F --> G
G --> H
H --> I
style A fill:#dbeafe,stroke:#2563eb,stroke-width:2px,color:#0f172a
style B fill:#e0f2fe,stroke:#0284c7,stroke-width:2px,color:#0f172a
style C fill:#ecfeff,stroke:#0891b2,stroke-width:2px,color:#0f172a
style D fill:#ede9fe,stroke:#7c3aed,stroke-width:2px,color:#0f172a
style E fill:#f3e8ff,stroke:#9333ea,stroke-width:2px,color:#0f172a
style F fill:#fae8ff,stroke:#c026d3,stroke-width:2px,color:#0f172a
style G fill:#fef3c7,stroke:#d97706,stroke-width:2px,color:#0f172a
style H fill:#ecfccb,stroke:#65a30d,stroke-width:2px,color:#0f172a
style I fill:#f0fdf4,stroke:#16a34a,stroke-width:2px,color:#0f172a