CReSIL

CReSIL detects and characterizes extrachromosomal circular DNA (eccDNA) from long-read sequencing data to map eccDNA sequences, structures, and genomic origins.

Key Features:

• Long-Read Sequencing Integration: Leverages long-read sequencing technologies to construct comprehensive maps of eccDNA and resolve repetitive genomic regions relevant to eccDNA structure.
• High Performance: Demonstrates a minimum F1 score of 0.98 on simulated data for eccDNA identification.
• Genomic Annotation Capabilities: Provides genomic annotation to infer functional roles of identified eccDNAs, including associations with oncogenes.
• Visualization Tools: Produces Circos visualizations to investigate eccDNA architecture and genomic relationships.

Scientific Applications:

• Cancer Research: Maps eccDNAs that harbor oncogenes to study mechanisms of tumorigenesis and to investigate potential biomarkers or therapeutic targets.
• Dataset Validation: Validated across multiple long-read sequencing datasets, including eccDNA-enriched datasets and whole-genome datasets from cells containing large eccDNA products.
• EccDNA Structural Studies: Enables investigation of both complex and simple eccDNA structures in eukaryotic cells.

Methodology:

Implements a construction-based rolling-circle-amplification approach for eccDNA sequence identification and location, analyzes long-read sequencing data, performs genomic annotation, and generates Circos visualizations.