danylmb/ggrasp repository overview

GGRaSP: a R-package for selecting representative genomes using Gaussian mixture models. Thomas H Clarke, Lauren M Brinkac, Granger Sutton, and Derrick E Fouts. Bioinformatics, bty300, https://doi.org/10.1093/bioinformatics/bty300⁠

GGRaSP (Gaussian Genome Representative Selector with Prioritization) is an R-package which can generate and return a reprentative set of genomes from a large group of genomes with a defined relationship. The reprentative set is select either using user-defined cutoff or cluster number values or else de novo calculates the clusters based on modeling the genome relationships with a Gaussian Mixture Model. The default value returned is the list of reprentative genomes, but the package also allows for multiple outputs including text files, plots, and trees. To allow for high-throughput analysis, we have included an Rscript file that can run GGRaSP from the command line (though it does require GGRaSP to be installed to the default R location).

The docker includes two ways GGRaSP can be used. The first uses the R-console to use the GGRaSP functions to load the genomes, cluster the genomes, and report the reprentative genomes. The second uses the command line Rscript.

• https://github.com/JCVenterInstitute/GGRaSP⁠

• https://cran.r-project.org/web/packages/ggrasp/index.html⁠