Biochef: a client-side WebAssembly-based workflow builder for genomic data analysis
Year: 2026
Type: article
Abstract: 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.
Source: BMC Bioinformatics
Authors: Joaquim Rosa, João Andrade, Jorge Miguel Silva, José Luis Oliveira
Institution: University of Aveiro
Language: English
Subfield: Information Systems and Management
Field: Decision Sciences
Domain: Social Sciences
Open Access status: gold
Estimated APC paid: $2,990
OpenAlex ID: W4415449203
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