gfakluge

gfakluge provides C++ parsing, writing, and conversion of Graphical Fragment Assembly (GFA) format files for manipulation and analysis of genome assemblies and sequence graphs.

Key Features:

• C++ library and command-line utilities: A C++ library and accompanying command-line utilities expose programmatic access and standalone operations for handling GFA files.
• Parsing and writing: Parses GFA files into structured in-memory data representations that expose fields and members, and writes GFA output.
• GFA version conversion: Converts between GFA format versions 0.1, 1.0, and 2.0 to maintain compatibility across tools.

Scientific Applications:

• Genome assembly and sequence graph analysis: Represents and manipulates sequence graphs and genome assemblies encoded in the GFA format.
• Interoperability and algorithm development: Enables exchange of GFA files among bioinformatics tools and supports development of graph-based genomics algorithms.

Methodology:

Parses GFA files into structured data representations of sequence graphs and performs GFA writing and conversion between versions 0.1, 1.0, and 2.0.