DAGReader

3D Interactive Visualization for Genome Assembly Graphs (GFA)

DAGReader is a desktop bioinformatics tool that reads Graphical Fragment Assembly (GFA) files and renders the underlying assembly graphs in three dimensions. It is inspired by Bandage but built from the ground up as a native 3D viewer with real-time layout, selection, and exploration.

Why DAGReader?

Genome assembly graphs can be massive, tangled, and difficult to reason about in 2D alone. DAGReader uses the GRIP (Graph dRawing with Intelligent Placement) algorithm to compute a 3D layout that you can fly through, inspect, and query interactively. Segments and links are rendered as Bézier tubes with full camera control, selection, and search.

The code has been optimized for efficiency and works well for large graphs.

Note

This project is under active development.

Features

• Native 3D rendering — OpenGL 4.3+ pipeline with tessellation and geometry shaders; edges are drawn as curved 3D tubes, not flat lines.
• GRIP layout engine — Multi-scale force-directed placement (Kamada–Kawai + Fruchterman–Reingold) accelerated with OpenMP.
• GFA v1.0 support — Parses segments, links, containments, and paths. Optional minimal memory mode skips large optional fields to help fit huge graphs in RAM.
• Interactive GUI (Dear ImGui) — Fully controllable side panel with:
  • Live layout parameter tuning (rounds, temperature, scaling)
  • Appearance controls (colors, widths, randomization)
  • Subgraph visibility & selection tables
  • Search by name (strict + fuzzy) across segments, links, paths, and containments
  • Dynamic coloring of segments by their properties (depth/length)
• Selection & inspection — Click to select segments/links; view metadata, sequence data, and CIGAR strings in floating HUDs.
• Camera controls — Free-fly, pan, rotate, zoom, and orbit around selections.
• Linux & Windows compatible — macOS planned down the line.

Quick Start

Dependencies

You only need CMake, git, and a C++20 compiler. All other dependencies (GLFW, GLEW, GLM, Dear ImGui, nativefiledialog-extended, spdlog, inipp) are fetched automatically via CMake FetchContent.

Platform	Install command
Debian / Ubuntu	sudo apt update && sudo apt install cmake git build-essential libomp-dev
Fedora	sudo dnf install cmake git gcc-c++ libomp-devel
Arch	sudo pacman -Syu cmake git base-devel openmp

Build

git clone https://github.com/G-rox-y/DAGReader.git
cd DAGReader

# Release build (recommended)
cmake -B build -S . -G "Ninja" -DCMAKE_BUILD_TYPE=Release
cmake --build build -j

Note

if the cmake step fails due to some missing dependencies, check out the Full Dependency Reference

Run

./build/DAGReader

Windows Build (MSYS2)

1. Install MSYS2 and open the UCRT64 shell.
2. Update the environment: pacman -Syu
3. Install toolchains:

   pacman -S --needed git mingw-w64-ucrt-x86_64-gcc mingw-w64-ucrt-x86_64-cmake mingw-w64-ucrt-x86_64-ninja

4. Build:

   cd /c/path/to/DAGReader
   cmake -S . -B build -G Ninja -DCMAKE_BUILD_TYPE=Release
   cmake --build build -j
   ./build/DAGReader.exe

Full Dependency Reference

If the minimal install above fails during the CMake configuration step, your system is likely missing the OS-level graphics, windowing, or desktop-integration libraries that cannot be fetched automatically.

What you need and why

Requirement	Needed by	Typical package names
CMake ≥ 3.24	Build system	cmake
Git	Fetching dependencies	git
C++20 compiler	The project itself	build-essential, gcc-c++, mingw-w64-ucrt-x86_64-gcc
OpenMP (optional)	GRIP layout acceleration	libomp-dev, libomp-devel, openmp
pkg-config / pkgconf	NFD, GLEW, GLFW discovery	pkg-config, pkgconf-pkg-config, pkgconf
OpenGL / Mesa dev headers	GLEW + OpenGL context	libgl1-mesa-dev, mesa-libGL-devel, mesa
X11 development libraries	GLFW on X11	libxrandr-dev, libxinerama-dev, libxcursor-dev, libxi-dev
Wayland dev libraries (optional)	GLFW on Wayland	libwayland-dev, wayland-protocols
GTK3 development files	nativefiledialog-extended (file dialogs on Linux)	libgtk-3-dev, gtk3-devel, gtk3

Per-distro copy-paste commands

Use the block that matches your distribution if the Quick Start table was insufficient.

Debian / Ubuntu / Mint

sudo apt update && sudo apt install -y \
  cmake git build-essential libomp-dev \
  pkg-config libgl1-mesa-dev \
  libgtk-3-dev \
  libxrandr-dev libxinerama-dev libxcursor-dev libxi-dev libxkbcommon-dev \
  libwayland-dev wayland-protocols

Fedora

sudo dnf install -y \
  cmake git gcc-c++ libomp-devel \
  pkgconf-pkg-config mesa-libGL-devel \
  gtk3-devel \
  libXrandr-devel libXinerama-devel libXcursor-devel libXi-devel libxkbcommon-devel \
  wayland-devel wayland-protocols-devel

Arch / Manjaro

sudo pacman -Syu --needed \
  cmake git base-devel openmp \
  pkgconf mesa \
  gtk3 \
  libxrandr libxinerama libxcursor libxi libxkbcommon \
  wayland wayland-protocols

Technical Overview

• Renderer: Custom OpenGL backend using programmable pipeline (vertex → tessellation control → tessellation evaluation → geometry → fragment). Edges are rendered as variable-width Bézier tube segments with normal-based lighting hints directly in the geometry shader.
• Layout: GRIP builds a hierarchy of filtered graphs and places vertices from coarse to fine, combining Kamada–Kawai neighborhood forces with Fruchterman–Reingold repulsion. Parameters are exposed in the UI for experimentation.
• Threading: Multi-threaded architecture with a dedicated window/render thread and a controller thread that handles file I/O, parsing, and layout computation. Communication is via a lock-free-ish channel with condition variables and atomics.
• Parser: Hand-written GFA parser with strict validation warnings. Can perform reverse-lookup by name, fuzzy matching, and on-demand sequence/CIGAR streaming.

License & Credits

DAGReader is licensed under the zlib License.

Created by Petar Dušević with mentorship from Krešimir Križanović.

Acknowledgments

The exsistance of the following open-source projects has greatly helped in the creation of DAGReader:

Project	Purpose
GLFW	Windowing and input handling
glew-cmake	OpenGL extension loading
GLM	Graphics math library
Dear ImGui	Immediate-mode GUI
nativefiledialog-extended	Cross-platform native file dialogs
spdlog	Fast C++ logging
inipp	Simple INI file parsing

The embedded UI font is Roboto Medium, distributed alongside Dear ImGui. Optional multithreading support is provided by OpenMP.

Get involved

The codebase has been written in a way that tries to minimize the amount of code while trying to keep things readable and manageable for the developer, this is done to invite contribution and should be respected in any pull requests.

If you have ideas, issues, or want to collaborate, feel free to open a ticket or a pull request.