Annotated Alignment Visualiser

A Vue 3 + Vite web application for visualizing DNA sequence alignment traces. Renders trace data with Plotly.js, including base call quality and alignment mismatches.

Features

• 📊 Interactive Plotly.js visualization
• 📁 Upload JSON alignment files
• 📥 Load a bundled example trace with its GenBank annotations
• 🔍 Zoom and pan with rangeslider
• 🎨 Color-coded nucleotide peaks (A/C/G/T)
• ❌ Highlight alignment mismatches
• 📱 Responsive design
• ⚡ Fast, built with Vite

Development

Prerequisites

• Node.js 16+
• npm or yarn

Setup

# Install dependencies
npm install

# Start development server
npm run dev

# Build for production
npm run build

# Preview production build
npm run preview

The development server will run at http://localhost:5173

Deployment to GitHub Pages

1. Update Repository Settings

1. Push your code to GitHub
2. Go to repository Settings → Pages
3. Set Source to "GitHub Actions"

2. Automatic Deployment

The included GitHub Actions workflow (.github/workflows/deploy.yml) will automatically:

• Build the Vue app with Vite
• Deploy to GitHub Pages on every push to main

3. Access Your App

Your app will be available at:

https://YOUR_USERNAME.github.io/annotated-align-visualiser/

Manual Deployment (if needed)

# Build the project
npm run build

# The 'dist' folder is ready to deploy

Then manually upload the dist folder contents to your hosting service.

Project Structure

├── src/
│   ├── main.js           # App entry point
│   ├── App.vue           # Root Vue component
│   └── renderer.js       # Plotly rendering logic
├── index.html            # HTML template
├── vite.config.js        # Vite configuration
├── package.json          # Dependencies
└── .github/workflows/    # GitHub Actions

Data Format

The app expects JSON files matching the Tracy/GEAR alignment format:

{
  "refchr": "chr1",
  "refpos": 100,
  "forward": true,
  "gappedTrace": {
    "peakA": [...],
    "peakC": [...],
    "peakG": [...],
    "peakT": [...],
    "basecallPos": [...],
    "basecallQual": [...],
    "basecalls": {...},
    "leadingGaps": 0
  },
  "refalign": [...]
}

License

MIT