sequence_breadth_tools

Purpose

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.

Dependencies

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