assembly-statsx

Browser-based genome assembly quality statistics — a client-side reimplementation of the Sanger Pathogens assembly-stats CLI with interactive visualisations and multi-file comparison.

Features

• Multi-file comparison — drop in up to 5 assemblies and compare side-by-side
• Full N-value suite — N10 through N100 with corresponding L-values
• Interactive charts — length histogram, N-value curve, cumulative length plot, contig size distribution, GC% distribution
• Export — download results as CSV or JSON
• Gzip support — accepts .fasta, .fa, .fq, .fastq, and .gz variants
• Pure client-side — no server, no WASM, no data leaves your browser

Statistics computed

Matches the CLI output: numSequences, totalBases, avgLength, medianLength, largest, smallest, N10–N100 with L-values, nCount, gaps, gcPercent

Getting started

npm install
npm run dev       # dev server at localhost:5173

Commands

Command	Description
npm run dev	Start Vite dev server
npm test	Run unit tests (vitest, 48 tests)
npm run build	Type-check + production build
npm run lint	ESLint
npm run check	Tests + lint + build

Tech stack

• Vite + React 18 + TypeScript — no CDN scripts
• Recharts — all charts
• DecompressionStream API — native browser gzip decompression

Project structure

src/
├── assembly-statsx/     # Domain logic (framework-free)
│   ├── types.ts         # Interfaces and defaults
│   ├── format.ts        # formatBases(), formatPct()
│   ├── parseFasta.ts    # FASTA/FASTQ parser with gzip support
│   ├── computeStats.ts  # N-values, GC, histograms, cumulative data
│   └── pipeline.ts      # Async orchestrator
└── components/          # React UI components

Part of GenomicX

This app is part of the GenomicX suite of browser-based bioinformatics tools.