Microbiome workflow — contamination and compositionality
Map a sequencing study with field blanks, extraction blanks and batch randomisation. Relative abundance is compositional; absolute microbial load requires a separately justified measurement.
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{
"nodes": [
{ "id": "field", "type": "rounded", "label": "Sampling design and covariates", "x": 40, "y": 200, "width": 150, "height": 104, "fill": "#ede9fe", "stroke": "#6d28d9" },
{ "id": "blank", "type": "octagon", "label": "Field and extraction blanks", "x": 215, "y": 520, "width": 150, "height": 104, "fill": "#e0f2fe", "stroke": "#0369a1" },
{ "id": "ext", "type": "rounded", "label": "Randomised extraction batches", "x": 215, "y": 200, "width": 150, "height": 104, "fill": "#fef3c7", "stroke": "#b45309" },
{ "id": "seq", "type": "rounded", "label": "Sequencing with controls", "x": 390, "y": 200, "width": 150, "height": 104, "fill": "#fef3c7", "stroke": "#b45309" },
{ "id": "qc", "type": "octagon", "label": "Read and contaminant QC", "x": 565, "y": 200, "width": 150, "height": 104, "fill": "#e0f2fe", "stroke": "#0369a1" },
{ "id": "tax", "type": "card", "label": "Taxonomic / functional profiles", "x": 740, "y": 200, "width": 150, "height": 104, "fill": "#ccfbf1", "stroke": "#0f766e" },
{ "id": "load", "type": "card", "label": "Optional absolute-load assay", "x": 565, "y": 520, "width": 150, "height": 104, "fill": "#ccfbf1", "stroke": "#0f766e" },
{ "id": "comp", "type": "rounded", "label": "Compositional analysis", "x": 915, "y": 200, "width": 150, "height": 104, "fill": "#fef3c7", "stroke": "#b45309" },
{ "id": "conf", "type": "rounded", "label": "Confounder sensitivity", "x": 915, "y": 520, "width": 150, "height": 104, "fill": "#f1f5f9", "stroke": "#475569" }
],
"edges": [
{ "id": "e0", "source": "field", "target": "ext", "label": "collect" },
{ "id": "e1", "source": "ext", "target": "seq", "label": "libraries" },
{ "id": "e2", "source": "blank", "target": "seq", "label": "control background" },
{ "id": "e3", "source": "seq", "target": "qc", "label": "reads" },
{ "id": "e4", "source": "blank", "target": "qc", "label": "identify artifacts", "style": "dashed" },
{ "id": "e5", "source": "qc", "target": "tax", "label": "retain profiles" },
{ "id": "e6", "source": "tax", "target": "comp", "label": "relative abundances" },
{ "id": "e7", "source": "load", "target": "comp", "label": "additional scale", "style": "dashed" },
{ "id": "e8", "source": "field", "target": "conf", "label": "covariates" },
{ "id": "e9", "source": "comp", "target": "conf", "label": "test robustness" }
]
}