SARS-CoV-2 Genomic Analysis Across US States

This repository contains an end-to-end notebook workflow for analyzing SARS-CoV-2 genomic sequences from California, New York, and Texas.

Project Scope

• Data extraction and filtering by state
• Sequence cleaning and FASTA export
• Alignment and guide-tree construction
• Consensus sequence generation
• Mutation hotspot visualization
• Comparative phylogenetic artifacts

Main Notebook

• bio-finall.ipynb
• Detailed run and output guide: OUTPUT_AND_RUN_GUIDE.md

Key Data and Output Folders

• CALIFORNIA
• NEWYORK
• TEXAS
• consenses

Typical Outputs

• State-specific cleaned CSV and FASTA files
• Consensus FASTA sequences
• Multiple sequence alignment artifacts
• Newick tree files (.nwk)
• Plot images (.png/.jpg)

Reproducibility

Install dependencies and run the notebook cells in order:

pip install -r requirements.txt
jupyter notebook

License

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