Using the Snakemake pipelines

Much more documentation to come...

This utilizes Snakemake, which is documented at https://bitbucket.org/johanneskoester/snakemake/wiki/Home

Note that Python 3.4 is required to use these tools with Snakemake.

Setting up an analysis directory

Configuring for your compute platform

Assembly of pre-filtered reads

Taxonomic filtration of raw reads

Starting from Illumina BCL directories