Biochef: a client-side WebAssembly-based workflow builder for genomic data analysis

Area of Science:

• Bioinformatics
• Computational Biology
• Web Technologies

Background:

• Genomic analyses traditionally require command-line tools on remote servers, posing challenges for non-expert users and raising data privacy issues.
• WebAssembly (WASM) technology allows native code execution within web browsers, removing the need for installations and data transfers.

Purpose of the Study:

• To introduce BioChef, a novel client-side platform designed to simplify genomic workflow execution using WebAssembly.
• To provide an intuitive, graphical user interface (GUI) for complex bioinformatics tasks, making them accessible to a broader audience.

Main Methods:

• BioChef compiles bioinformatics toolkits into browser-executable modules.
• A drag-and-drop GUI facilitates workflow creation with real-time validation and flexible input options (form-based and JSON).
• Workflows can be exported as bash scripts or configuration files for reproducibility.

Main Results:

• Performance benchmarks across major browsers show fast loading (LCP 0.583s) and responsive interaction (INP 30.5ms).
• While slower than native execution (~130x), BioChef workflows are significantly faster (11.3x) than traditional web services like Galaxy due to eliminated network delays and server queueing.
• The platform demonstrates minimal layout shifts (CLS 0.01) with acceptable WASM module load times.

Conclusions:

• BioChef successfully leverages client-side WebAssembly to democratize genomic data processing.
• The platform enhances privacy, reproducibility, and user-friendliness without external dependencies.
• This represents the first fully client-side, graphical genomic workflow environment powered by WASM.