.. VMI Bootcamp II documentation master file, created by
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Welcome to the Second VMI Bootcamp!
===========================================


.. figure:: ./images/vmi_logo.jpeg
   :scale: 70 %
   :alt: vmi_logo


**November 9th, 2018**

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   :maxdepth: 2
   
   ./rst/location



**An introduction to microbiota community analysis**

   - Organized by the `Vanderbilt Microbiome Initiative (VMI) <https://my.vanderbilt.edu/microbiome/>`_ and funded by `Vanderbilt University Trans-Institutional Programs (TIPs) <https://www.vanderbilt.edu/strategicplan/trans-institutional-programs/tipshome.php>`_
   - Founded By - Members of the Dept. Biological Sciences, Peabody college, School of Engineering, and the Medical Center
   - Research – 160 Vanderbilt scholars across 5 schools committed to fundamental and translational microbiome research
   - Education and Training – Campus-wide programs to deploy state-of-the-art tools to propel microbiome research
   - Ongoing Clinical Trial - Multi'omic, dietary intervention, temporal sampling, multi-ethnic

**Goals:**

   1. Understand the importance of good experimental design 

   2. Explore the critical steps in a typical microbiome amplicon sequencing analysis

   3. Utilize the QIIME2 pipeline to process microbiome datasets
   
Microbiome Introduction
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   ./rst/1_microbiome_introduction

Experimental Design and Sample Preparation
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   ./rst/2_experimental_design

Turning Sequences into Community Composition
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   ./rst/3_sequences_to_composition

Concepts of Community Analysis
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   ./rst/4_concepts_of_community_analysis

Analyzing Microbial Communities and Hypothesis Testing
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   ./rst/5_analysis_and_hypothesis_testing


Command Line Tutorial
----------------------

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   ./rst/command_line_introduction

Other Resources
===============

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`