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Simple desktop downloads

WGSExtract v6 Alpha

A preview desktop app for working with whole-genome sequencing files. Pick your platform and install the latest alpha build.

Earlier WGSExtract alpha desktop app showing the FASTQ workflow in GUI for CLI.
Earlier alpha interface shown; v0.6.5 adds the workflows described below.

Current alpha release: v0.6.5, bundling WGSExtract CLI v0.6.5. Includes native Windows setup, opt-in MultiQC reports, expanded microarray/AADR exports, and targeted Y analysis. See available workflows or full release notes.

Windows install note

If SmartScreen appears, continue in two clicks.

WGSExtract v6 Alpha is new, free, open-source software. Microsoft Defender SmartScreen can warn about newer apps until enough people have downloaded and run them. If you downloaded the installer from this project, press More info, then Run anyway.

Step 1

Press More info.

Windows SmartScreen warning with the More info link visible
Step 2

Press Run anyway.

Windows SmartScreen warning after expanding details, showing the Run anyway button

Install and start

  • Windows (x64): run the .exe installer, then launch WGSExtract. If SmartScreen appears, follow the steps above only for an installer downloaded from this project's releases.
  • macOS: choose Apple Silicon or Intel, open the .dmg, and drag WGSExtract to Applications. The app and disk images are signed and notarized.
  • Linux (x86_64): make the AppImage executable (chmod +x WGSExtract_0.6.5_amd64.AppImage) and run it, or install the .deb, .rpm, or Arch package with your distro's package manager.

On first launch, run the bundle's setup to install the pinned CLI and its runtime tools; downloads need a network connection. Windows CLI setup runs natively without WSL or MSYS2. Reference data and optional tools have separate requirements; install the resources needed for your chosen workflow before running it. Linux and Windows ARM64 desktop installers are not yet published.

Release builds support signed self-updates. macOS also offers File > Uninstall to remove setup, app data, and the app.

Related rough sites

This site and the WGSExtract CLI website are rough AI-generated websites while WGSExtract v6 Alpha is still being assembled.

More information

The download page stays intentionally small. The GUI for CLI project background, architecture notes, and documentation map live on the other pages.

WGSExtract story Architecture Documentation