16S analysis for "Assessment of the NASA Standard Spore Assay in Predicting Bacterial Populations of a Mars Mission Assembly Facility".
- code
This directory contains the code (as notebooks) for each step in a numerically organized format. More descriptions can be found within the README file for that directory.
- data
This directory contains the input data, along with some output from computationally expensive tools.
Source tracking done with the entirety of the Earth Microbiome and American Gut projects is not included in this repository due to size (analysis in code/2.1.0-time-source-variation.ipynb). However, the data tables for that sourcetracking step can be re-generated through redbiom with code within code/2.1.0-time-source-variation.ipynb.
- results
The main and extended figures and tables from the paper which can be reproduced by running the notebooks within the code directory.
There are two options for setup to run the notebooks.
The first option is a QIIME 2019.10 environment amended with any additional plugins. This option is preferable for OSX users. The conda yml file is provided in environment/jpl-environment.yml. Installation of the environment can be done through conda env create -n saf-pp-jpl --file environment/jpl-environment.yml.
With the environment installed and activated each notebook can be run and populate the results directory with all of the extended tables and figures used in the paper.