mmgenome2 is an R-package designed to facilitate reproducible extraction of individual genomes from metagenomes. It is an implementation of the different binning strategies described in the multi-metagenome project, and makes it possible to apply these to any metagenome data. In combination with the RMarkdown format, the mmgenome2 package allows for reproducible step-by-step extraction of high-quality genomes from metagenomes as well as generating publication-ready figures with minimal effort.

First, install R (3.4.3 or later) and RStudio. Windows users should also install RTools, make sure the PATH checkbox is checked during installation. Then open RStudio as administrator (!) and run the following commands (just copy/paste) to install mmgenome2 from the console:

#check for remotes
if(!require(remotes))
  install.packages("remotes")
  
#install mmgenome2 using remotes
remotes::install_github("kasperskytte/mmgenome2")

To install mmgenome2 on MAC please see this before running the above commands.

For a brief guide about the basics of mmgenome2 go to the Get Started page.