Description: A primary goal of microbial Genome Wide Association Studies is identifying genomic variants associated with habitats. Existing tools fail to identify known causal variants if the analyzed trait (like habitat adaptation) shaped the phylogeny. Due to the presence of allochthonous strains or metadata errors the stated sources of microbial strains in public databases are often incorrect. We developed a new tool aurora (https://github.com/DalimilBujdos/aurora) that identifies autochthonous strains and the genes associated with habitats while acknowledging the potential role of the trait in shaping the phylogeny. We successfully validated aurora by applying it to simulated datasets, and multiple species with various traits.
Installation
You can install the development version of aurora from GitHub with:
# install.packages("devtools")
devtools::install_github("DalimilBujdos/aurora")For instructions on how to use the package, please refer to vignettes