Professional FASTQ Quality Analysis Tool with Modern Web Interface

Phastats is a comprehensive bioinformatics tool that provides detailed quality control analysis for FASTQ sequencing data. It offers both command-line and web-based interfaces with interactive visualizations and professional reporting capabilities.

Try it now: phastats-demo-8328e0496479.herokuapp.com

Upload your FASTQ files and get instant professional analysis results!

Full Documentation: somtoik.github.io/phastats

• Comprehensive Analysis: Quality scores, sequence lengths, GC content, and per-base content analysis
• N50 Calculation: Genome assembly quality metric not available in FastQC
• Dual Interface: Both command-line tool and modern web application
• Responsive Design: Professional, mobile-friendly web interface
• Interactive Visualizations: High-quality plots and charts
• Multiple Output Formats: HTML, JSON, CSV, and TSV reports
• High Performance: Optimized algorithms for large file processing
• Docker Ready: Containerized for easy deployment

phastats/
├── phastats-main/phastats/    # Command-line tool & PyPI package
│   ├── src/phastats/          # Core Python modules
│   ├── tests/                 # Test suite
│   ├── setup.py               # Package configuration
│   └── pyproject.toml         # Modern Python config
├── phastats-web/              # Web application
│   ├── app.py                 # Flask web server
│   ├── templates/             # HTML templates
│   ├── static/                # CSS & assets
│   ├── Dockerfile             # Container config
│   └── requirements.txt       # Dependencies
├── docs/                      # GitHub Pages website
│   ├── index.html             # Landing page
│   └── getting-started.html   # Documentation
└── .github/workflows/         # CI/CD pipeline

Visit the Live Demo - no installation required!

# Install from PyPI (when published)
pip install phastats

# Or install from source
git clone https://github.com/somtoik/phastats.git
cd phastats/phastats-main/phastats
pip install -e .

# Run analysis
phastats input.fastq

git clone https://github.com/somtoik/phastats.git
cd phastats/phastats-web
pip install -r requirements.txt
python app.py

cd phastats-web
docker build -t phastats-web .
docker run -p 5000:5000 phastats-web

• Quality Distribution: Per-base quality scores and statistics
• Length Analysis: Sequence length distribution with N50
• GC Content: Per-sequence GC analysis and bias detection
• Per-Base Content: Base composition across read positions
• Summary Statistics: Comprehensive quality metrics

• Backend: Python, Flask, NumPy, Pandas, SciPy, Matplotlib
• Frontend: HTML5, Bootstrap 5, JavaScript
• Deployment: Heroku, Docker
• CI/CD: GitHub Actions
• Documentation: GitHub Pages

• Production-ready deployment on Heroku
• Professional documentation with GitHub Pages
• Automated CI/CD pipeline with GitHub Actions
• Docker containerization for easy deployment
• Comprehensive test suite with pytest
• Code quality tools (Black, Flake8, MyPy)
• Modern Python packaging (setuptools, pyproject.toml)
• Responsive web design for all devices

• Python 3.7+
• Dependencies: Flask, NumPy, Pandas, SciPy, Matplotlib
• Browser: Modern browser for web interface
• Memory: Scales with file size (optimized for large files)

Contributions are welcome! Please see CONTRIBUTING.md for guidelines.

This project is licensed under the MIT License - see the LICENSE file for details.

somtochukwu Ikeanyi

• GitHub: @somtoik
• Email: [email protected]

• Live Demo: phastats-demo-8328e0496479.herokuapp.com
• Documentation: somtoik.github.io/phastats
• PyPI Package: pypi.org/project/phastats (coming soon)
• Docker Hub: hub.docker.com/r/somtoik/phastats-web (coming soon)

If you find this project useful, please consider giving it a star!