madansix

Contig Scaffolding via Pan-Genome Synteny — in your browser

madansix is a browser-based implementation of madansi, reordering and reorienting fragmented bacterial genome assembly contigs using pan-genome gene synteny.

Features

• Pan-genome guided contig scaffolding
• Minimap2 alignment via WebAssembly (biowasm)
• Interactive contig connectivity visualisation (D3.js)
• Before/after N50 statistics
• Client-side processing — no data leaves your browser

Usage

1. Upload your assembly FASTA
2. Upload your pan-genome reference FASTA (from Roary)
3. Upload your pan-genome graph (.dot, from Roary)
4. Click Run Scaffolding
5. Download the reordered assembly FASTA

Development

npm install
npm run dev

Testing

npm run test         # unit tests
npx playwright test  # E2E tests

Docker

docker build -t madansix .
docker run -p 8080:80 madansix

Credits

• Original madansi tool: Joanna Tumelty, Wellcome Sanger Institute
• Web app: Andrew Page

License

GPL-3.0-only