myoga

Map Your Own Genomics Atlas

myoga is a local-first tool for geographically visualizing parsnp outbreak datasets.

It lets users explore phylogenomic trees, sample metadata, and geographic locations in a Microreact-like interface while keeping genomic and metadata files on their own machine.

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Why build myoga?

myoga is designed for local review of sensitive outbreak datasets.

During normal use:

• users select files from their own machine
• files are kept in local browser memory
• the app is served from 127.0.0.1
• no myoga server receives genomic files or metadata
• release builds work without external setup

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Quick Start

The easiest way to use myoga is to download a release.

1. Go to the Releases page.
2. Download the ZIP file for your operating system.
3. Unzip it.
4. Run the myoga executable.

Platform examples:

• Windows: double-click myoga.exe
• macOS/Linux: double-click or run ./myoga

myoga starts a local server on:

127.0.0.1

Then it opens the app in your default browser.

No Python, Node.js, or command-line setup is required for release builds.

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What You Load

myoga uses three local files from a Parsnp analysis:

• parsnp.ggr
• parsnp.tree
• a metadata table for the genomes in the Parsnp run

The app keeps these files in browser memory and does not upload genomic data, metadata, coordinates, or outbreak files anywhere.

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What myoga Shows

myoga provides an interactive local view of:

• genome/sample locations on a map
• the Parsnp phylogenomic tree
• linked sample metadata
• optional local GeoJSON geography layers
• bundled offline map data

It is intended for confidential, case-by-case outbreak review where data should remain local.

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Example Data

To get a better look at what myoga can do use the example data in the assets/mers49 folder.

The example opens in an offline globe view. Users can switch between globe and flat map modes, inspect tree structure, view metadata, and test the interface without providing their own files.

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Documentation

Longer documentation is available in the project wiki.

• Metadata file creation
• Supported metadata columns
• Custom GeoJSON layers
• Troubleshooting

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Notes

• parsnp.tree is used as the authoritative source for phylogenetic labels.
• parsnp.ggr is read locally and used to cross-check genome names from the Parsnp/Gingr project file.
• myoga includes bundled map assets for offline-friendly use.
• Custom local GeoJSON layers can be loaded for outbreak-specific geography.

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Author

Austin G. Marshall