https://github.com/aaronmussig/gtdb-phylogenetic-diversity
Snakemake pipeline to calculate the phylum phylogenetic diversity of GTDB R220.
Science Score: 13.0%
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Low similarity (5.1%) to scientific vocabulary
Repository
Snakemake pipeline to calculate the phylum phylogenetic diversity of GTDB R220.
Basic Info
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Metadata Files
README.md
gtdb-phylogenetic-diversity
Snakemake pipeline to calculate the phylogenetic diversity of each phylum in GTDB R220.
Dependencies
The only dependency is Snakemake (version >= 7.32.4) which is assumed to be on the command line.
Installation
Clone the repository:
bash
git clone git@github.com:aaronmussig/gtdb-phylogenetic-diversity.git
cd gtdb-phylogenetic-diversity
Running the pipeline
To run the pipeline, simply execute the following command:
bash
snakemake --use-conda --cores all
Pipeline steps
- Trees and taxonomy files for the Archaeal and Bacterial domains are downloaded.
- Both trees are scaled by their relative evolutionary divergence (RED) using PhyloRank.
- A script will then calculate the phylogenetic diversity of each phylum in GTDB R220 by the sum of their branch lengths.
Both the RED and non-scaled trees will produce values.
Output files are saved under: ./output/
Owner
- Name: Aaron Mussig
- Login: aaronmussig
- Kind: user
- Location: Brisbane, Australia
- Company: Australian Centre for Ecogenomics
- Twitter: aaronmussig
- Repositories: 7
- Profile: https://github.com/aaronmussig
Bioinformatics PhD student at the University of Queensland. Python and Rust enthusiast.
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