gfabase | GFA insert into GenomicSQLite

gfabase is a Jupyter Notebook library. gfabase has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. You can download it from GitHub.

gfabase is a command-line tool for indexed storage of Graphical Fragment Assembly (GFA1) data. It imports a .gfa file into a compressed .gfab file, from which it can later access subgraphs quickly (reading only the necessary parts), producing .gfa or .gfab. Beyond ID lookups, .gfab indexes the graph by mappings onto reference genome coordinates, facilitating navigation within de novo assemblies and pangenome reference graphs. Effectively, .gfab is a new GFA-superset format with built-in compression and indexing. It is in fact a SQLite (+ Genomics Extension) database populated with a GFA1-like schema, which programmers have the option to access directly, without requiring gfabase nor even a low-level parser for .gfa/.gfab.