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Run and Output Guide

This document explains how to run the SARS-CoV-2 analysis workflow and where to find the final outputs.

Project Goal

Analyze SARS-CoV-2 genomic sequences for three US states:

  • California
  • New York
  • Texas

Main workflow notebook:

  • bio-finall.ipynb

Requirements

Install Python dependencies:

pip install -r requirements.txt

Recommended environment:

  • Python 3.10+
  • Jupyter Notebook or VS Code Notebook

How To Run

  1. Open bio-finall.ipynb
  2. Run cells from top to bottom in order
  3. Do not skip preprocessing cells because downstream steps depend on generated files
  4. If a cell uses an absolute local path, replace it with your local project path

Expected Core Outputs

After successful execution, these folders and files are the key outputs.

State-specific outputs

  • CALIFORNIA/

    • cleaned_California_data.csv
    • sequences.fasta
    • california_msa.fasta
    • consensus_california.fasta
    • tree_from_scratch.nwk
    • California_mutation_hotspot.png

  • NEWYORK/

    • cleaned_New_York_data.csv
    • sequences.fasta
    • newyork_msa.fasta
    • consensus_newyork.fasta
    • tree_from_scratch.nwk
    • New York_mutation_hotspot.png

  • TEXAS/

    • cleaned_Texas_data.csv
    • sequences.fasta
    • texas_msa.fasta
    • consensus_texas.fasta
    • tree_from_scratch.nwk
    • Texas_mutation_hotspot.png

Combined/final outputs

  • consenses/
    • consensus_california.fasta
    • consensus_newyork.fasta
    • consensus_texas.fasta
  • final_consensus_tree.png
  • phylogenetic_tree_cleaned.png

Quick Validation Checklist

Use this checklist after running the notebook:

  • All three cleaned CSV files exist in CALIFORNIA, NEWYORK, TEXAS
  • All three consensus FASTA files exist in consenses
  • At least one .nwk tree file exists per state folder
  • final_consensus_tree.png and phylogenetic_tree_cleaned.png are generated

Notes

  • The repository excludes unrelated contour/pipe image artifacts by design.
  • One very large file was intentionally excluded from version control to satisfy GitHub limits.