https://github.com/robaina/genome_selector
https://github.com/robaina/genome_selector
Last synced: about 1 year ago
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- Host: GitHub
- URL: https://github.com/robaina/genome_selector
- Owner: Robaina
- License: apache-2.0
- Created: 2024-08-22T12:23:06.000Z (almost 2 years ago)
- Default Branch: main
- Last Pushed: 2025-03-26T13:05:03.000Z (about 1 year ago)
- Last Synced: 2025-04-06T10:38:00.056Z (about 1 year ago)
- Language: Jupyter Notebook
- Size: 149 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
- License: LICENSE
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README
## Select a subset of representative genomes from traits matrix and abundances
This package selects a genome subset of size _k_ from traits matrix (genomes vs presence/absence of enzymes) and relative abundances, such that functional diversity (enzyme set) is maximized and the selected genomes are representative of the entire community.
### Use case
This package was developed as a means to select representative genomes to build commnunity genome-scale metabolic models (cGEMs), representative of microbial communities found in metagenomic samples. cGEMs are composed of biochemical reactions at their core, hence the need to optimize for enzyme (i.e. reaction) diversity.