16s rRNA

Yuwei BaoNovember 15, 2023

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

  • 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.


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

  1. https://onlinelibrary.wiley.com/doi/abs/10.2307/1218190open in new window ↩︎

  2. https://www.nature.com/articles/s41596-022-00738-yopen in new window ↩︎ ↩︎