CircleSeeker is a specialized bioinformatics pipeline designed for the identification, classification, and characterization of extrachromosomal circular DNA (eccDNA) from PacBio HiFi long-read sequencing data.

Key features: - Dual-engine support: Cresil (preferred) and Cyrcular (fallback) with intelligent auto-selection - Hybrid detection strategy combining tandem repeat detection with Split-Read assembly - Comprehensive eccDNA classification (UeccDNA, MeccDNA, CeccDNA, XeccDNA) - Automated pipeline with checkpoint and resumption capabilities - Detailed HTML reports and comprehensive output formats - Modular architecture with 16 processing steps