Trace analyzer

Open-source analysis tool for data from Agilent DNA/RNA analysis instruments

No hardware control yet; this software only reads and analyses saved runs.

This software needs testing. TapeStation support needs work. Please report other issues

Supported instruments

Platform	Native format	Status
Bioanalyzer 2100	.xad	Native .xad opens as raw detector channels plus available assay/sample fields; exported .xml/.xml.gz opens with processed traces, peaks, sizing, concentration, molarity, and RIN.
TapeStation	.D1000/… (encrypted ZIP)	Native project files are encrypted; exported .xml + _Electropherogram.csv pairs open with traces, peaks, sizing, per-peak quantities, integrity values, and region bounds.
Fragment Analyzer	.raw + .PKS sidecars	Partial native reader: .raw CCD traces, .txt well/sample names, .PKS size anchors and peak tables. Concentration/molarity are computed from the standard ladder setpoints and decoded peak areas.

A note on Bioanalyzer .xad files: a native .xad stores the raw detector signal and limited sample/assay fields only. 2100 Expert recomputes the processed per-well traces, peaks, sizing and RIN each time it opens the file — only its exports (File → Export to XML, PDF) capture those numbers. So today, opening a .xad shows the raw electropherograms and available source fields, while opening an exported .xml shows the full processed results. Reproducing the vendor's numbers from a raw .xad is on the roadmap.

Getting started

Requires a Rust toolchain. Build and open a file with:

# GUI viewer — accepts .xad (native raw channels), .xml/.xml.gz, TapeStation CSV, FA .fa.zip/.raw:
cargo run -- path/to/run.xad

To try it without your own data, download the bundled demo runs and open one:

bash scripts/fetch-testdata.sh
cargo run -- testdata/demo_dna1000.xml.gz

Running the GUI needs a working display. On Linux you may also need X11/Wayland and GTK development packages; see docs/development.md for prerequisites, headless use, and the command-line inspect tool.

Installing

CI builds downloadable artifacts for Windows, Linux, and macOS on pushes, pull requests, tags, and manual workflow runs. GitHub workflow-run artifacts may be downloaded as artifact archives; extract them to get the actual Windows .zip, Linux .deb, or macOS .zip. Tag release assets expose those .zip/.deb files directly. The Windows .zip contains one .exe, the Linux .deb is native-architecture, and the macOS .zip contains the universal Intel + Apple Silicon .app bundle.

Linux — install the release binary, a .desktop launcher entry, MIME rules for native files, and the app icons into a standard freedesktop layout, so Trace analyzer shows up in your application menu:

make deb                         # → target/deb/trace-analyzer_<version>_<arch>.deb
sudo make install                # into /usr/local (default)
make install PREFIX="$HOME/.local" # per-user, no sudo

make uninstall (with the same PREFIX) removes them again. Packagers can stage into a build root with DESTDIR. make deb derives versioned ELF library dependencies with dpkg-shlibdeps; packagers can override DEB_ARCH, DEB_DEPENDS for extra non-ELF dependencies, or DEB_RECOMMENDS when building a package. Desktop portals are recommended for portal-backed file dialogs.

macOS — build a double-clickable app bundle (with icon):

make osx-app                     # → target/osx/Trace analyzer.app
make osx-app-universal           # Intel + Apple Silicon bundle

Documentation

• docs/architecture.md — code layout, the .xad reader, and how calibration works.
• docs/xad_format.md — reverse-engineered .xad container and schema specification.
• docs/fa_format.md — reverse-engineered Fragment Analyzer .raw/.PKS notes and current reader limitations.
• docs/development.md — building, testing, fixtures, and packaging.

Credits

Format knowledge and demo data derive from the MIT-licensed R packages jwfoley/bioanalyzeR and grimbough/bioanalyzeR.