CodonAnalyzer

Originally developed using Perl in 2015, this pipeline has been modernized in 2025 with reproducibility and modularity in mind.

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Features

• Codon usage statistics and GC content
• Longest ORF extraction
• Protein sequence translation
• Hydropathy calculation (Kyte–Doolittle)
• Plotting via Python + Matplotlib
• Configurable via config.yaml
• Reproducible workflow using Snakemake

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Quickstart

git clone https://github.com/yourusername/codonanalyzer.git
cd codonanalyzer

Setup Environment

conda install -c conda-forge -c bioconda snakemake matplotlib numpy=1.26.0

or using environment.yml:

conda env create -f environment.yml 

Then, run:

snakemake --cores 1

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Documentation

See the full documentation here.

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Author

Abhinav Mishra
Email: [email protected]

For full historical context, see About.

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License

BSD 3-Clause. See LICENSE.