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: - CtcReads-Core: TideHunter-based confirmed eccDNA detection - SplitReads-Core: Built-in split-read inference (HiFi optimized) - 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