16s rRNA

According to protocol paper for Kraken 2, Bracken, KrakenUniq, and KrakenTools (published Sept 28, 2022): "Metagenome analysis using the Kraken software suite"

• Kraken: classify microbiome samples

• Bracken : estimate abundance of microbiome samples (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

Terminology

• $\alpha$-diversity: a measure defined by Whittaker ^[1] captures the average diversity within a particular ecosystem. There are different $\alpha$-diversity values that approximate the average diversity by computing a sort of weighted average for species counts in a sample. ^[2]
• $\beta$-diversity is useful when trying to examine the change in species diversity between two or more ecosystems. ^[2:1]

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1. https://onlinelibrary.wiley.com/doi/abs/10.2307/1218190 ↩︎

2. https://www.nature.com/articles/s41596-022-00738-y ↩︎ ↩︎