Tools for extracting sequence breadth data from an Anvi'o profile database (tested with v7.1) and using it to evaluate the presence and absence of bacterial populations according to a user-provided cutoff. Includes scripts for making figures and performing statistical tests.
All of the following are included in the sequence-breadth-tools.yml file.
The easiest way to install them is by creating a conda environment with the following command:
conda env create -f sequence-breadth-tools.yml
matplotlib 3.5.3
numpy 1.21.6
pandas 1.3.5
scipy 1.3.1
sqlite 3.30.0
statannotations 0.6.0