4. 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.

4.1. Setting up an analysis directory

4.2. Configuring for your compute platform

4.3. Assembly of pre-filtered reads

4.4. Taxonomic filtration of raw reads

4.5. Starting from Illumina BCL directories