https://github.com/kellylab/sequence_breadth_tools
Extracting and analyzing sequence breadth from Anvi'o databases
https://github.com/kellylab/sequence_breadth_tools
Last synced: 4 months ago
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Extracting and analyzing sequence breadth from Anvi'o databases
- Host: GitHub
- URL: https://github.com/kellylab/sequence_breadth_tools
- Owner: kellylab
- License: gpl-3.0
- Created: 2024-09-06T14:34:15.000Z (almost 2 years ago)
- Default Branch: main
- Last Pushed: 2024-11-21T19:33:34.000Z (over 1 year ago)
- Last Synced: 2024-11-21T20:28:20.458Z (over 1 year ago)
- Language: Python
- Homepage:
- Size: 33.2 KB
- Stars: 0
- Watchers: 4
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 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