MLSTX

Browser-based Multi-Locus Sequence Typing — no server required.

MLSTX is a WebAssembly clone of tseemann/mlst. Drop in one or more bacterial genome assemblies in FASTA format and get sequence type assignments in seconds. Scheme detection is fully automatic — MLSTX identifies the most likely scheme from your assembly, runs the allele alignments, and assigns a sequence type, all in one step. No installation or data upload required.

Features

• Auto-detects MLST scheme from your assembly — no scheme selection needed
• 162+ schemes covering major bacterial pathogens (from PubMLST via tseemann/mlst)
• Exact, novel, partial, and missing allele calls with clear visual badging
• Multi-sample batch processing — upload and type any number of assemblies at once
• Neighbour-joining phylogenetic tree from concatenated allele alignment (2+ samples)
• CSV export of all results
• Works offline after first load — scheme databases are cached in your browser

Tech Stack

• minimap2 — sequence alignment (via Aioli/biowasm WebAssembly)
• FastTree — phylogenetic tree inference (WebAssembly)
• React + Vite — frontend framework
• Cloudflare Pages — global CDN hosting

Getting Started

npm install
npm run dev

Open http://localhost:5173

Running Tests

npm test           # unit tests
npm run test:e2e   # end-to-end tests (requires build first)

Contributing

Contributions welcome. Please open an issue first to discuss changes.

License

GPL-3.0 — see LICENSE