RonaQC

Browser-based quality control for SARS-CoV-2 sequencing data — no data upload required.

RonaQC processes BAM files from ARTIC and similar pipelines entirely in the browser using WebAssembly. It assesses cross-contamination, primer contamination, and consensus sequence quality to determine whether samples are suitable for phylogenetic analysis and submission to public databases (GISAID / INSDC). Your BAM files are never uploaded to any server.

Features

• ARTIC primer scheme support (V1 through V5.4.2)
• Negative control QC — detects cross-contamination via SNP and amplicon analysis
• Sample QC — genome completeness, ambiguous bases, longest N run
• Amplicon coverage heatmap for visual QC across samples
• Per-sample genome-wide coverage plots
• Actionable judgements aligned with PHA4GE QC guidelines (Upload / Use only / Discard)
• CSV/TSV export for all reports
• Optional subsampling (30K reads) for faster processing

Tech Stack

• samtools — BAM processing and coverage statistics (via biowasm WebAssembly)
• ivar — primer trimming and consensus calling (via biowasm WebAssembly)
• D3.js — interactive coverage plots and amplicon heatmaps
• React + Vite — frontend framework
• Cloudflare Pages — global CDN hosting

Getting Started

npm install
npm run dev

Open http://localhost:5173

Running Tests

npm test           # unit tests
npm run test:e2e   # end-to-end tests (requires build first)

Citation

Alikhan, N-F. (2022). RonaQC: Quality control of SARS-CoV-2 genomic data.
https://github.com/happykhan/ronaQC

Contributing

Contributions welcome. Please open an issue first to discuss changes.

License

GPL-3.0 — see LICENSE