BiNgoViewer 2.5.3

BiNgo Genome Viewer — a lightweight browser-based genomics viewer

BiNgo Genome Viewer

A lightweight, browser-based genomics viewer for visualizing genomes, coverage tracks, read alignments, variants, and annotations. Built as a modern alternative to IGV.

Supported File Formats

Type	Formats
Genome	GenBank (.gb, .gbk), FASTA (.fasta, .fa)
Coverage	BigWig (.bw), WIG (.wig), BedGraph (.bedgraph, .bdg)
Reads	BAM (.bam + .bai index)
Variants	VCF (.vcf, .vcf.gz)
Annotations	BED (.bed), GFF (.gff, .gff3), GTF (.gtf), GenBank (.gb)

Quick Start

Requires Python 3.10 or newer. Download from python.org if needed.

Install with pip (recommended)

No Node.js required — the frontend is pre-built and bundled.

pip install BiNgoViewer
bingo

Options:

bingo                    # launch on default port 8000
bingo --port 9000        # use a custom port
bingo --no-browser       # start without opening the browser
bingo --install          # create a desktop shortcut
bingo --update           # check for updates
bingo --version          # show installed version
bingo --no-update        # skip automatic update check

Windows (one-click)

Double-click Install_Windows.bat. It will install Python dependencies into a local environment and launch the viewer. No command line needed.

macOS / Linux (one-click)

Double-click Install_macOS.command (or run it from a terminal). It will create a virtual environment, install dependencies, and launch the viewer.

Permission denied? Run once in Terminal:

chmod +x Install_macOS.command

Docker

No Python or Node.js required — everything runs inside the container.

cd app
docker compose up --build

Then open http://localhost:8000.

Troubleshooting

Problem	Solution
python not found	Install Python 3.10+ and check Add to PATH during setup
"No matching distribution"	Your Python is too old — BiNgo requires Python 3.10+. Check with python --version
pip install fails	Try pip install --user BiNgoViewer or use a virtual environment
Port 8000 in use	Run bingo --port 9000 (or any free port)
Browser doesn't open	Visit http://localhost:8000 manually
Server won't stop	The server auto-exits when you close all browser tabs; or press Ctrl+C

Usage

1. Load files — Use the file picker, drag and drop, or paste a local file path (recommended for large BAM files).
2. Navigate — Left-click drag to pan, scroll to zoom, use the chromosome scrubber to jump across the genome.
3. Select regions — Right-click drag to select a region; hover for stats (coverage, variants, reads).
4. Zoom to gene — Double-click a gene annotation to zoom in with context.
5. Track settings — Adjust height, color, scale, bar width, peak outline trace, and nucleotide display.
6. Reorder tracks — Drag the grip handle on any track label.
7. Export — Save the current view as SVG or PNG with layered groups.
8. Save session — Export/restore your entire workspace including zoom, colors, and settings.
9. Save session — Store your workspace and restore it later.

API Documentation

When the server is running, interactive API documentation is available at:

• Swagger UI: http://localhost:8000/docs
• ReDoc: http://localhost:8000/redoc

Project Structure

├── Install_Windows.bat         # Windows installer (double-click)
├── Install_macOS.command       # macOS / Linux installer (double-click)
├── README.md
├── pyproject.toml              # pip package definition
├── bingoviewer/                # Installable Python package
│   ├── cli.py                  # `bingo` CLI entry point
│   ├── server/                 # FastAPI backend (bundled)
│   └── frontend_dist/          # Pre-built React frontend
└── app/                        # Application source code
    ├── backend/                # Python (FastAPI) REST API
    └── frontend/               # React (Vite) user interface

Citation

If you use this software in your research, please cite:

Ngo, B.M. (2026). BiNgo Genome Viewer (v1.8.2) [Software].

References & Acknowledgments

Click to expand

Software Dependencies

Backend

• FastAPI — Ramírez, S. (2018). FastAPI: A modern, fast web framework for building APIs with Python. https://fastapi.tiangolo.com/
• Uvicorn — Encode OSS. ASGI server implementation for Python. https://www.uvicorn.org/
• BioPython — Cock, P.J.A. et al. (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25(11), 1422–1423.
• pyfaidx — Shirley, M.D. et al. (2015). Efficient "pythonic" access to FASTA files using pyfaidx. PeerJ PrePrints, 3:e1196.
• bamnostic — Sherman, M.A. & Mills, R.E. (2019). BAMnostic: a pure Python, OS-agnostic Binary Alignment Map (BAM) file parser and random access tool.

Frontend

• React — Meta Platforms, Inc. A JavaScript library for building user interfaces. https://react.dev/
• Vite — You, E. (2020). Next generation frontend tooling. https://vitejs.dev/
• Axios — HTTP client for the browser and Node.js. https://axios-http.com/

File Format Specifications

• SAM/BAM — Li, H. et al. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25(16), 2078–2079.
• VCF — Danecek, P. et al. (2011). The variant call format and VCFtools. Bioinformatics, 27(15), 2156–2158.
• BigWig/WIG — Kent, W.J. et al. (2010). BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics, 26(17), 2204–2207.
• BED — UCSC Genome Browser, University of California, Santa Cruz.
• GFF3 — Sequence Ontology Project. Generic Feature Format Version 3.
• GTF — Ensembl genome database project.
• GenBank — Benson, D.A. et al. (2013). GenBank. Nucleic Acids Research, 41(D1), D36–D42.

Inspiration

• IGV — Robinson, J.T. et al. (2011). Integrative Genomics Viewer. Nature Biotechnology, 29(1), 24–26.

Acknowledgments

Early version testing and feedback:

• Amanda Antoch
• Isaac Poarch
• Otto Chipashvili
• Jake Colautti

License

All rights reserved. Contact the author for licensing inquiries.