Additional file 2 of The host genotype actively shapes its microbiome across generations in laboratory mice

Additional file 2. Analysis repository. We performed all the presented analysis and graph generation through a single jupyter notebook. It lists necessary dependencies for full reproducibility. We have outsourced some of the functions into a public 16s rRNA gene analysis code repository: https://github.com/sjanssen2/ggmap. By default, external system calls are submitted to a Slurm cluster. You can instead run on your local machine by providing the optional argument use_grid=False. Additional conda environments can be conveniently created via "cd recipes && make all-env" after cloning the above repository and changing into its working directory. All files necessary for our analysis, the jupyter notebook and a static HTML version of the jupyter notebook for ease of readability are packaged as one zip compressed file