GraphBin visualise WebAssembly App

A browser-based interactive visualisation tool for comparing initial metagenomic binning results and GraphBin-refined binning results on assembly graphs.

This project uses Pyodide (Python compiled to WebAssembly) to run igraph, GraphBin’s graph visualisation code, and the plotting code entirely in the browser — no backend needed.

Web App (Anyone can use)

Please go to metagentools.github.io/graphbin-visualise-wasm-app/ for a live demo hosted on GitHub Pages.

No installation needed! Python not required. Node.js not required. You only need a modern browser such as Chrome, Firefox, Safari or Edge.

Features

• Run GraphBin plotting fully in the browser using WebAssembly
• Supports SPAdes assembler layout (GFA, contigs FASTA, contig paths). Support for MEGAHIT and Flye is coming soon.
• Upload your initial binning + GraphBin binning results
• Adjustable plot settings:
• Automatically renders two plots: 1) initial binning plot and 2) GraphBin-refined binning plot
• Client-side file handling — your data never leaves your computer
• Download generated plots
• Built-in test data for immediate demonstration
• Pure static site — works on GitHub Pages.

Technologies Used

• Pyodide (Python → WebAssembly)
• igraph (graph processing + plotting)
• matplotlib (Pyodide backend) for image generation
• JavaScript for UI + FS bridging
• HTML/CSS user interface
• GraphBin plotting logic

Running the App Locally (Advanced)

Clone the repository:

git clone https://github.com/metagentools/graphbin-visualise-wasm-app.git
cd graphbin-visualise-wasm-app

Because the browser cannot fetch local files with file:///, you must serve it with a lightweight local server. You will need Python for this step.

python -m http.server 8000

Then copy and paste the following link in your web browser.

http://localhost:8000

Citation

If you use this in your work, please cite GraphBin, GraphBin-Tk (full citations below) and the Wasm ABABCS2025 Workshop (doi: https://doi.org/10.5281/zenodo.17743837).

Vijini Mallawaarachchi, Anuradha Wickramarachchi, Yu Lin. GraphBin: Refined binning of metagenomic contigs using assembly graphs. Bioinformatics, Volume 36, Issue 11, June 2020, Pages 3307–3313, DOI: https://doi.org/10.1093/bioinformatics/btaa180

Mallawaarachchi et al., (2025). GraphBin-Tk: assembly graph-based metagenomic binning toolkit. Journal of Open Source Software, 10(109), 7713, https://doi.org/10.21105/joss.07713

Funding

This work is funded by an Essential Open Source Software for Science Grant from the Chan Zuckerberg Initiative.