ruchira / gbwt-rs

GBWT in Rust

GBWT (in Rust)

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
• Locate queries

GBWTGraph / 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 construction
• GBWT merging
• Cached GBWT

Notes

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