MUSiCC: A marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome [article]

Ohad Manor, Elhanan Borenstein
2014 biorxiv/medrxiv   pre-print
Functional metagenomic analyses commonly involve a normalization step, where measured levels of genes or pathways are converted into relative abundances. Here, we demonstrate that this normalization scheme introduces marked biases both across and within human microbiome samples and systematically identify various sample- and gene-specific properties that contribute to these biases. We introduce an alternative normalization paradigm, MUSiCC, which combines universal single-copy genes with
more » ... y genes with machine learning methods to correct these biases and to obtain a more accurate and biologically meaningful measure of gene abundances. Finally, we demonstrate that MUSiCC significantly improves downstream discovery of functional shifts in the microbiome. MUSiCC is available at http://elbo.gs.washington.edu/software.html.
doi:10.1101/009407 fatcat:bafywtmpe5efpdlif57776pavi