Microbiome analysis

Scripts for software install and analysis for microbiome datasets

QIIME2

• qiime2install.txt: code for qiime2 software installation

  • customized for JetStream BioLinux instances
  • installs Miniconda, QIIME2, and dependencies

• The following scripts set up project directories, and perform the basic analysis:

  • moving-pictures-qiime2.sh: script for general workflow using qiime2
  • moving-pictures-qiime2export.sh: script for exporting data from qiime2 for import to R

  R

  • phyloseq-qiime2.R: imports data, performs statistical tests, and visualizes results