SKIN METAGENOMICS ANALYSIS GUIDE

This repository contains the analyses as described in:

Biogeography and individuality shape function in the human skin
metagenome 

Julia Oh, Allyson L. Byrd, Clay Deming, Sean Conlan, NISC
Comparative Sequencing Program, Heidi H. Kong, and Julia A. Segre 
Nature 514, 59–64 (2014).

Contact: [email protected]

Disclaimers: 
1. Please note that these are not really downloadable
"programs" per se. Each group of scripts represent workflows for
processing raw read data underlying the analyses published in the paper.
Hence, these are works in progress and are undergoing rapid iteration!

2. We believe that every dataset and analysis is unique and thus please
keep this in mind as you use these workflows. For instance, if you have
really deep sequencing data with few samples, our assembly and binning
methods will probably not be your best bet. If you are interested in
something specific we did, please leave a comment and we will try to get
back to you.

3. We can make no commitment beyond an amorphous endeavor to actively
update associated databases, although we promise to upload databases if
we do update them. However, most can be expanded in a fairly
straightforward way, if you have specific references in mind.

4. The workflow was designed on a GNU/Linux parallel processing system
with access to nodes with >256GB RAM, <32 processors/node, and 500GB
temp disk space. Some analyses will run on smaller machines, and others
will need to be adapted. We have tried to indicate where excessive
amounts of RAM is needed.



A brief description of the contents:

assembly/
Adaptive and iterative assembly for samples with variable
coverage.

genecatalog/
Creation of non-redundant multi-kingdom skin gene catalog.

metagenomic_clusters/
Clustering genes to create metagenomic linkage
groups, i.e., metagenomic ‘species’, meta-‘genome’, pan-genome, etc.

read_processing/
Our basic pipeline for processing reads generated
through use of Nextera libraries.

strain_mapping/
Studying strain-level heterogeneity in species with a
well-characterized sequence space.

taxonomy/
Multi-kingdom (bacterial, fungal, viral) taxonomic mapping and
abundance estimations.