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

Joaquim Rosa1, João Andrade2, Jorge Miguel Silva3

  • 1IEETA/DETI, LASI, University of Aveiro, Campus Universitário de Santiago, Aveiro, 3810-193, Portugal. joaquimvr15@ua.pt.

BMC Bioinformatics
|April 10, 2026
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Summary
This summary is machine-generated.

BioChef, a new platform using WebAssembly (WASM), enables client-side genomic data processing directly in web browsers. This approach enhances privacy, reproducibility, and ease of use for non-technical users, bypassing traditional server-based limitations.

Keywords:
Bioinformatics workflowsGenomic data processingHuman-computer interactionWeb-based applicationsWebAssemblyWorkflow management systems

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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.