BioChef

BioChef compiles bioinformatics tools to WebAssembly to enable client-side genomic data analysis workflow construction and execution directly in web browsers without data upload.

Key Features:

• WebAssembly Compilation: Bioinformatics tools including samtools, minimap2, bcftools, bedtools, seqtk, fastp, and GTO are compiled to WebAssembly and execute on the user's local computer.
• Workflow Construction: Workflows are built through a graphical interface and shared as a single JSON file.
• Signed Tool Bundles: Tools are published as signed bundles in the BioChef Registry and verified in the browser before execution.
• Flexible Input Methods: The system supports both form-based and JSON input methods for workflow configuration.
• Intermediate Step Inspection: Users can inspect intermediate steps during workflow execution.
• Reproducible Export: Workflows can be exported as bash scripts or configuration files for reproducibility.
• Real-time Validation: The system provides real-time validation during workflow construction and execution.

Scientific Applications:

• Genomic Data Analysis: End-to-end genomic data processing workflows are executed entirely in the browser without server-side computation or data transfer.
• Privacy-Preserving Analysis: Sensitive genomic data remains on the user's local machine, eliminating privacy concerns associated with remote server execution.
• Reproducible Research: Workflows exported as JSON configuration files or bash scripts enable sharing and reproduction of analytical pipelines.

Methodology:

Bioinformatics tools are compiled to WebAssembly using Emscripten, loaded as WASM modules in the browser, and orchestrated through a client-side workflow engine; performance was benchmarked across Chromium, Gecko, and WebKit browser engines using standard genomic pipelines.