QIIME2

In development - Will be used to automate processing of Illumina reads generated from 515F and 806R 16S libraries using Qiime2 tools.

To run full pipline:

snakemake --use-conda --cores 16

To run only raw processing:

snakemake results/raw/demux-trimmed.qza --use-conda

To rerun stats with a new depth:

vim config/stats.yaml snakemake results/stats/core-diversity --use-conda