GfaPy

GfaPy provides Python-based creation, parsing, and editing of sequence graphs to represent assembly, variation, and splicing graph structures in GFA 1 and GFA 2 formats.

Key Features:

• Format Support: Native support for GFA 1 and GFA 2 with capabilities for interconversion between the two versions.
• Sequence Graph Operations: Creation, parsing, and editing of sequence graph records and structures.
• Custom Record Types: Definition and management of GFA 2 custom record types for extending graph semantics.
• Python Library: Implemented as an extensible Python library for programmatic manipulation of GFA graphs.
• Biological Graph Representation: Explicit handling of assembly graphs, variation graphs, and splicing graphs as graph data structures.

Scientific Applications:

• Genome Assembly: Representation and manipulation of assembly graphs used in genome assembly workflows.
• Variation Analysis: Representation of variation graphs to support studies of genetic diversity and mutation analysis.
• Transcriptomics: Representation of splicing graphs to support analysis of alternative splicing and transcript structures.

Methodology:

Parsing, creation, and editing of GFA 1 and GFA 2 sequence graphs; interconversion between GFA versions; and definition/management of GFA 2 custom record types via an extensible Python API.