Phylogenetic placement workflow demonstration files

Introduction

This is a collection of files used to demonstrate the use of a phylogenetic placement-based workflow. It can be used on the linux or OS X platforms, and for windows users it works great on the QIIME virtual box. A reasonably recent laptop with 2GB of memory should be able to run this code just fine if you don't have too many other things open.

Setup

This demo can be downloaded here. You will need to download the v1.1 pplacer suite as well. There is a download.sh script in the bin directory which will get it, or you can visit the pplacer website.

You will then need to put pplacer, guppy, and rppr in your path.

SQLite

SQLite3 is only necessary for one part of the demo. It is already installed on recent OS X macs. If you want to install it on an Debian/Ubuntu system (e.g. the QIIME virtual box) just run an

sudo apt-get install sqlite3

QIIME users: the password is qiime.

Running

Simply execute the script pplacer_demo.sh. This script was meant to be read, and pplacer_demo.html is a marked up version of it.

Authors

Noah Hoffman, Aaron Gallagher and Erick Matsen.

Acknowledgements

The data for this demonstration was generated as part of ongoing work at the Fred Hutchinson Cancer Research Center on the microbiome of the vagina. We would like to thank Martin Morgan, Sujatha Srinivasan and David Fredricks for their work and for allowing the data to be used.