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.
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