glickmac / Microbiome_Demo

A repository containing a demo microbiome workflow for R and Python

Microbiome_Demo

Table of Contents

What is the Microbiome?
Workflow
Installing Tools
Workflow Usage

What is the Microbiome?

The microbiome is a collection of all microorganisms in a niche. For the purposes of this demo, we focus solely on the bacterial microbiome. The bacterial microbiome is accessible via a universally conserved gene sequence called the 16s ribosomal RNA.

Microbiome Workflow

To identify the bacterial taxa in a niche, a region of the 16s ribosomal RNA gene is amplified and sequenced. This repository stores two workflows to analyze the resulting 16s sequences though more information about the workflows and additional techniques can be found:

• Dada2

• Qiime2

Installing Items for Workflows

Software:

Optional but highly recommended method to install Qiime using Anaconda

• Anaconda: download

• Qiime w/ Anaconda (On Command-Line):

wget https://data.qiime2.org/distro/core/qiime2-2018.2-py35-osx-conda.yml
conda env create -n qiime2-2018.2 --file qiime2-2018.2-py35-osx-conda.yml

## Optional Cleanup 
rm qiime2-2018.2-py35-osx-conda.yml

• Jupyter Notebook:

pip install jupyter

• Bioconductor (In R Environment):

source("https://bioconductor.org/biocLite.R")
biocLite()

• Dada2 and other packages:

source("https://bioconductor.org/biocLite.R")
biocLite("dada2")
biocLite("phyloseq")
install.packages("RColorBrewer")
install.packages("ggplot2")

• R Kernal for Jupyter Notebook: See installation instructions for IRKernel here or directly from the github repository

Additional instructions for installing the required packages are found within the demo scripts.

Using Microbiome Workflows

This repository holds two jupyter workflows one in R (Dada2 & Phyloseq) and one in python (Qiime2). This repsoitory is a guide and a working demo tutorial. To use the workflows on your own system follow the instructions below.

• Download this repository

• Unzip and move into repository

cd Microbiome_Demo-master/

• Activate QIIME Environment on Commandline

source activate qiime2-2018.2

• Start Jupyter Notebooks

jupyter notebook