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Background <p>Genomics analyses often rely on command-line tools executed via remote servers, imposing usability barriers for non-technical users and raising privacy concerns. WebAssembly (WASM) enables native-code execution directly in web browsers, eliminating installations and data transfers.</p> Results <p>We introduce BioChef, a client-side genomic workflow platform that uses WASM. BioChef compiles a genomics toolkit into browser-executable modules and exposes them through a drag-and-drop GUI designed to be intuitive. The system provides real-time validation, flexible input methods (form-based and JSON), intermediate step inspections, and reproducible workflows exportable as bash scripts or configuration files. Performance benchmarks across major browsers (Chromium, Gecko, WebKit) demonstrate rapid initialization (LCP 0.583 s), responsive interactivity (INP 30.5 ms), minimal layout shifts (CLS 0.01), and acceptable overhead (average 181.5 ms initial WASM module load). Although browser execution introduced performance penalties (<InlineEquation ID="IEq1"> <EquationSource Format="TEX">\(\sim \)</EquationSource> <EquationSource Format="MATHML"><math> <mo>∼</mo> </math></EquationSource> </InlineEquation>130<InlineEquation ID="IEq2"> <EquationSource Format="TEX">\(\times \)</EquationSource> <EquationSource Format="MATHML"><math> <mo>×</mo> </math></EquationSource> </InlineEquation> slower than native), BioChef workflows still significantly outperformed traditional web services such as Galaxy by avoiding network delays and server-side queueing (11.3<InlineEquation ID="IEq3"> <EquationSource Format="TEX">\(\times \)</EquationSource> <EquationSource Format="MATHML"><math> <mo>×</mo> </math></EquationSource> </InlineEquation> faster in a standard pipeline benchmark).</p> Conclusions <p>BioChef shows how WebAssembly on the client side can democratize genomic data processing, ensuring privacy, reproducibility and ease of use without external dependencies. To our knowledge, this is the first fully client-side, graphical genomic workflow environment powered by WASM.</p>

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

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年4月9日

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  • Joaquim Rosa,
  • João Andrade,
  • Jorge Miguel Silva,
  • José Luis Oliveira

摘要

Background

Genomics analyses often rely on command-line tools executed via remote servers, imposing usability barriers for non-technical users and raising privacy concerns. WebAssembly (WASM) enables native-code execution directly in web browsers, eliminating installations and data transfers.

Results

We introduce BioChef, a client-side genomic workflow platform that uses WASM. BioChef compiles a genomics toolkit into browser-executable modules and exposes them through a drag-and-drop GUI designed to be intuitive. The system provides real-time validation, flexible input methods (form-based and JSON), intermediate step inspections, and reproducible workflows exportable as bash scripts or configuration files. Performance benchmarks across major browsers (Chromium, Gecko, WebKit) demonstrate rapid initialization (LCP 0.583 s), responsive interactivity (INP 30.5 ms), minimal layout shifts (CLS 0.01), and acceptable overhead (average 181.5 ms initial WASM module load). Although browser execution introduced performance penalties ( \(\sim \) ∼ 130 \(\times \) × slower than native), BioChef workflows still significantly outperformed traditional web services such as Galaxy by avoiding network delays and server-side queueing (11.3 \(\times \) × faster in a standard pipeline benchmark).

Conclusions

BioChef shows how WebAssembly on the client side can democratize genomic data processing, ensuring privacy, reproducibility and ease of use without external dependencies. To our knowledge, this is the first fully client-side, graphical genomic workflow environment powered by WASM.