AgViz

AgViz is a browser-based viewer for genome assembly graphs in GFA format.

Use it online:

Open AgViz

AgViz lets you load a GFA file, view the assembly graph, and inspect segments and links without installing desktop software.

Key Features

• Open GFA files directly in your browser.
• Drag and drop a .gfa file, use the file picker, or try the bundled examples.
• View segments as curved contigs with endpoint-only links between them.
• Use the Bandage-style layout by default for familiar assembly graph browsing.
• Switch layouts when needed, including fCoSE, circle, concentric, CoSE, breadthfirst, and grid.
• Scale segment lengths with graph-normalised log10 scaling so the shortest and longest contigs in the loaded graph define the visual length range.
• Switch visual length modes between Log, Linear, and Uniform.
• Colour contigs by coverage when coverage tags are present.
• Click segments and links to inspect their metadata.
• See true bp lengths in the inspector, even when visual lengths are scaled for readability.
• Use light or dark theme.

What You Can Inspect

For segments, AgViz shows:

• segment ID
• true length in bp
• coverage, when available
• degree
• sequence preview
• GFA tags

For links, AgViz shows:

• source and target segments
• orientations
• overlap / CIGAR
• represented reciprocal link records
• raw link records, when available
• GFA tags

GFA Support

AgViz currently supports the core GFA 1 records needed for graph viewing:

Record	Support
H	Header tags are parsed and stored
S	Segments, sequence, length, coverage tags
L	Links, orientations, overlap/CIGAR
P	Paths are parsed but not yet visualised
Other	Stored with warnings, not visualised

Coverage can be read from common tags such as DP, KC, RC, and FC.

Example Graphs

The web app includes small example graphs:

• tiny.gfa - two segments connected by one link
• simple_cycle.gfa - three segments forming a cycle
• branching_graph.gfa - a root segment with two branches converging on a tip

Privacy

AgViz runs in your browser. For normal use, GFA files are read locally by the web app and are not uploaded to a server.

Run Locally

npm install
npm run dev

Open http://localhost:5173 in your browser.

Useful commands:

Command	Description
npm install	Install dependencies
npm run dev	Start the development server
npm run build	Build for production
npm test	Run tests
npm run preview	Preview the production build

Project Structure

src/
  gfa/          GFA parser and graph conversion
  graph/        Graph model, Cytoscape adapter, styles, layouts
  components/   React UI components