This is an IPython notebook I created to provide my colleagues and collaborators with a copy of my basic analysis workflow for analyzing microbial community sequence data using QIIME. This workflow starts with quality-filtered, de-multiplexed 16S rDNA sequences and a mapping (metadata) file, and ends with some basic diversity analysis output.
I hope this is useful, and I’d love feedback, especially of the “why the hell are you doing it like that?” variety.
I am hosting it on GitHub (a first for me.)
http://jennomics.github.io/QIIMEbyJennomics/
Disclaimer: I tested my notebook using the files that I’ve provided, and it worked for me. I use QIIME (macqiime) and IPython notebook for my research, and I used online tutorials to figure out how to use these tools. I am not a software developer or an IT support person or even a trained computer scientist.
Beginners can get started with these:
http://www.wernerlab.org/software/macqiime
http://nbviewer.ipython.org/github/ipython/ipython/blob/2.x/examples/Notebook/Index.ipynb
jennomics 