domains / families / science / abundance-estimation

abundance-estimation

separate

Turns shotgun classifier output into a defensible abundance table with Bracken Bayesian re-estimation, then compositional treatment (CLR, zero handling), library-size normalization, reference-frame differential abundance, and optional absolute quantification. Covers why a relative-abundance change is not a change, why Bracken read fractions and MetaPhlAn percentages are different physical quantities, the silent -r read-length bias, the genome-size confound no library-size method fixes, and the rarefaction debate. Use when estimating species abundance from a Kraken2 report, normalizing a community count table, choosing a compositional transform, or converting relative to absolute load. For classification see kraken-classification; for diversity/ordination/DA mechanics see metagenome-visualization.

When to use

• estimating species abundance from a Kraken2 report
• normalizing a community count table
• choosing a compositional transform
• converting relative to absolute load
• Bracken Bayesian re-estimation
• reference-frame differential abundance
• handling zero values in abundance data
• library-size normalization

When not to use

• classification
• diversity/ordination/DA mechanics
• generic 16S diversity

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