Resolution-Optimised SNPs Searcher

This is a R implementation of "Minimum SNPs" software as described in "Price E.P., Inman-Bamber, J., Thiruvenkataswamy, V., Huygens, F and Giffard, P.M." (2007) "Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants."

minSNPs Package

For manual, see here.

This is a rebuilt version of minSNPs. Its functionality is similar to the original repository, but has cleaner code and less dependencies.

The package has a dependency that is not in CRAN, but in BioC. In order for R to install that, you need to enable BioC repository, this can be done by running setRepositories() and selecting both CRAN & BioC Software.

This is a simple install script for R packages:

if (!require("minSNPs", quietly = TRUE)){
  if (!require("BiocParallel", quietly = TRUE)){
    if (!require("BiocManager", quietly = TRUE)){
      install.packages("BiocManager")
    }
    BiocManager::install("BiocParallel")
  }
  install.packages("minSNPs")
}

See standard workflow or standard workflow in Google colab for quick start.