README.md

Pipelines to generate files for figure 4(b) and various misc

This folder contains four snakemake pipelines to analyze the PLASS-assembled neighborhoods. These pipelines generate the content in Figures 4a and 4b, as well as some appendix tables and figures.

Clustering workflow

See this file for details. The clustering workflow corresponds to the red path through the DAG located in the appendix.

Variant workflow

See this file for details. The variant workflow corresponds to the yellow path through the DAG located in the appendix.

KEGG workflow & bin prokka

See this file for details. The KEGG workflow and the bin prokka workflow correspond to the red path through the DAG located in the appendix.