GBZ file format for pangenome graphs

March 26, 2026 ยท View on GitHub

This is a Rust reimplementation of parts of the GBWT and the GBWTGraph. It is based on the Simple-SDS library.

Scope

GBWT

  • Simple-SDS file format
  • Iteration over paths
  • Unidirectional search
  • Bidirectional search
  • Metadata
  • Construction
  • Locate queries

GBZ

  • Simple-SDS file format
  • Iteration over nodes and edges
  • Iteration over segments and links
  • Iteration over paths and path extensions
  • GFA extraction

Possible future extensions

  • GBWT/GBZ merging
  • Cached GBWT

Notes

  • The included .cargo/config.toml sets the target CPU to native.
  • See Simple-SDS for assumptions on the environment.