ECCsplorer

ECCsplorer detects extrachromosomal circular DNAs (eccDNAs) from paired-end Illumina sequencing of amplified circular DNA (circSeq) to identify enriched circular DNA elements for studies of genomic variation, organelle mini-circles, transposable elements, and disease-related eccDNA.

Key Features:

• Versatility Across Organisms: Analyzes circSeq data from any organism or tissue using next-generation sequencing, including Illumina datasets.
• Paired-end circSeq Processing: Processes paired-end read data derived from amplified circular DNA to enable eccDNA detection.
• Reference-based Read Mapping: Maps reads to a reference genome and detects informative read distributions such as high coverage regions, discordant mappings, and split reads.
• Reference-free Read Cluster Comparison: Compares read clusters from amplified eccDNAs against control sample data to identify specifically enriched DNA circles without a reference genome.
• Modular Workflow: Provides mapping-based and reference-free modules that can be run independently or combined.
• Detection Performance: Demonstrated ability to detect eccDNA candidates with high sensitivity and specificity, including mitochondrial mini-circles and activated retrotransposons.
• Dataset Compatibility: Handles semiartificial and published circSeq datasets, including examples from Homo sapiens, Arabidopsis thaliana, and Beta vulgaris.

Scientific Applications:

• Cancer Research: Identification and analysis of cancer-associated eccDNAs to study their roles in oncogenesis and cancer progression.
• Organelle Genomics: Detection and characterization of mitochondrial and other organelle-specific mini-circles.
• Transposable Element Studies: Identification of activated retrotransposons and other transposable elements present in eccDNA structures.
• Biological Process Studies: Investigation of eccDNA involvement in stress response, aging, and other genomic variation processes.

Methodology:

Processes paired-end Illumina circSeq data using a two-part analysis: (1) mapping reads to a reference genome to detect high coverage regions, discordant mappings, and split reads, and (2) reference-free comparison of read clusters from amplified eccDNAs against control samples to identify specifically enriched DNA circles; compatible with semiartificial and published circSeq datasets.