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README.md

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-# [Module-Name]
+# Pangenomics
 ---------------------------------
 
 ## **Contents**
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 ## **Overview**
 
+This module will introduce you to (graphical) pangenomics and walk you through a pangenomics pipeline.
+Specifically, you will learn how to build a pangenome graph, map reads to the graph, call variants on the mapped reads, and visualize the graph.
+All analyses will be performed on the Google Cloud Platform.
+The estimated cost for the complete module is $?
+
 
 ## **Background**
 
+A *pangenome* is a collection of genomes from the same species.
+Compared to a reference genome, a pangenome is a less biased, more comprehensive representation of sequence preservation and variation within a population.
+While the pangenome may provide greater insight into questions related to the genetic and genomic nature of a species, these data require the use of bioinformatics tools that are different than those typically used on reference genomes.
+This module aims to introduce you to the idea of *pangenome graphs* and the bioinformatics tools used for their analysis.
+
 
 ## **Before Starting**
 
+This module is designed to run on the Google Cloud Platform (GCP).
+Follow the instructions below to prepare to run the module on GCP.
+
+<details>
+
+<summary>Setting up GCP</summary>
+
+* Create a Google Cloud account
+* Create a Google Cloud project
+* Enable billing for your Google Cloud project
+* Create a Vertex AI Workbench instance
+* Clone this repository into your Workbench instance
+
+</details>
+
 
 ## **Getting Started**
 
+To begin, we must understand how this repository is organized.
+```
+└── module_notebooks/
+    ├── 00-environment-setup.ipynb
+    ├── 01-intro-to-pangenomics.ipynb
+    ├── 02-building-graphs-with-pggb.ipynb
+    ├── 03-indexing-graphs-with-vg.ipynb
+    ├── 04-read-mapping-with-vg.ipynb
+    ├── 05-variant-calling-with-vg.ipynb
+    ├── 06-searching-graphs-with-blast.ipynb
+    └── 07-visualization.ipynb
+```
+
+`module_notebooks/` contains Jupyter notebooks - one for each submodule.
+To open a notebook, simply double-click on it in your Workbench instance.
+To begin this module, open the `00-environment-setup.ipynb` notebook.
+This notebook will introduce you to Jupyter notebooks and instruct you on how to install the software for this module.
+
 
 ## **Software Requirements**
 
+The follow software is required for this module and will be installed as part of the `00-environment-setup.ipynb` submodule:
+
+* [PGGB](https://github.com/pangenome/pggb)
+* [vg](https://github.com/vgteam/vg)
+* [BLAST](https://www.ncbi.nlm.nih.gov/books/NBK569861/)
+* [Bandage](https://rrwick.github.io/Bandage/)
+
 
 ## **Architecture Design**