DeBreak

DeBreak detects and characterizes structural variations (SVs) from long-read sequencing data (PacBio and Oxford Nanopore) to enable accurate SV discovery, reconstruction of long insertions, and single base-pair breakpoint resolution.

Key Features:

• Analysis of long-read alignments: Operates on alignment results from PacBio and Oxford Nanopore long-read sequencing data.
• Density-Based Clustering: Clusters structural variation candidates using a density-based approach to group similar SVs.
• Local De Novo Assembly: Performs local de novo assembly to reconstruct long insertions.
• Partial Order Alignment Algorithm: Applies a partial order alignment algorithm to refine SV breakpoints to single base-pair resolution.
• K-Means Clustering for Multi-Allelic Events: Uses k-means clustering to identify and report multi-allelic SV events.

Scientific Applications:

• Cancer genomics: Identifies potentially tumor-driving structural variations in cancer genomes.
• Genome assembly augmentation: Supplements whole-genome assembly methods by detecting and characterizing structural variants and long insertions.

Methodology:

Analyzes alignment results from long-read sequencing (PacBio, Oxford Nanopore) and integrates density-based clustering of SV candidates, local de novo assembly for long insertions, partial order alignment for single base-pair breakpoint refinement, and k-means clustering for multi-allelic event reporting.