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gfaestus - Vulkan-accelerated GFA visualization

Demo: https://youtu.be/TOJZeeCqatk

gfaestus is a tool for visualizing and interacting with genome graphs in the GFA format.

It can display GFA graphs using a provided 2D layout (produced with odgi's layout command), and is intended to deliver an interactive visual interface for exploring genome graphs that is fast, powerful, and easy to use.

In addition to the 2D layout, a handlegraph representation of the GFA is created, which will enable visualizations and interactivity that take advantage of the graph topology, paths, and more.

gfaestus uses Vulkan for hardware-acceleration, via the ash crate.

Requirements

Compiling gfaestus requires the Vulkan SDK, available here: https://vulkan.lunarg.com/sdk/home

To run gfaestus, you must have a GPU with drivers that support

Vulkan. If you're on Windows or Linux, and have an AMD, Nvidia, or integrated Intel GPU, you should be good to go.

If you're on Mac, you'll need to install MoltenVK.

Usage

With a working Vulkan SDK environment (make sure you have glslc on your path), you can build gfaestus using cargo.

cargo build --release

Due to technical reasons, gfaestus must be run from the repo directory for shaders and scripts to be found. An easy way to do this is to use the generated shell script, which can be copied to your PATH:

./gfaestus-release <GFA> <layout TSV>

# use whichever directory on your path you like
cp gfaestus-release ~/.local/bin/gfaestus
gfaestus <GFA> <layout TSV>

Instructions

The easiest way to display annotations is via the BED Label Wizard under Tools in the top menubar.

You can also load a custom TSV format, which makes it easy to assign colors and labels to nodes.

Each line assigns either a color, in CSS-style hexadecimal format, or a text string, to a node. For example, for node 1223:

1223 #44BBCC
1223 this line is a label

Keyboard

  • Space: Reset view
  • Arrow keys: Pan view
  • Escape: Clear selection
  • F9 - Toggle light/dark mode

Mouse

  • Left Mouse: Select node

  • Left Mouse (click and drag): Pan view

  • Shift + Left Mouse (click and drag): Rectangle select

  • Scroll wheel: Zoom view

  • Right Mouse: Context menu