SDG

SDG implements Sequence Distance Graphs to integrate genome graphs and sequencing data for genome assembly and graph-based analyses.

Key Features:

• Graph Integration: Operates on genome assembly graphs and supports working with both raw sequencing reads and assembled genomes.
• Data Handling: Supports paired, linked, and long reads from diverse sequencing technologies.
• deBruijn Graph Module: Includes a simple deBruijn graph module to assist genome assembly tasks.
• Graph Importing (GFA): Imports graphs in the Graphical Fragment Assembly (GFA) format.
• Read Mapping: Maps raw reads onto graphs to enable analysis of sequencing data in a graph-based context.
• Python API: Provides a Python API to navigate the graph, access mapped and raw data, and perform scripted or interactive analyses.

Scientific Applications:

• Scaffolding: Scaffolds short read graphs with long reads to improve assembly contiguity.
• Heterozygous Graph Navigation: Navigates paths within heterozygous graphs to resolve allelic variation and complex structures.
• Trio Dataset Analysis: Applied to a simulated parent-offspring trio dataset for resolving complex genomic structures and variations.

Methodology:

Decouples mapping from analysis, enabling construction of multi-stage pipelines that can be dumped to and loaded from disk.