eccDNA-pipe

eccDNA-pipe processes high-throughput sequencing data to identify and analyze extrachromosomal circular DNA (eccDNA) from WGS, Circle-seq, and Circulome-seq using short- and long-read technologies.

Key Features:

• Comprehensive analysis pipeline: Integrates upstream and downstream analyses for end-to-end processing of eccDNA sequencing data.
• Sequencing platform support: Supports whole-genome sequencing (WGS), Circle-seq, and Circulome-seq from both short-read and long-read technologies.
• Quality control: Performs quality control measures on raw sequencing data prior to downstream analysis.
• eccDNA identification: Applies algorithms to detect and identify eccDNA from high-throughput sequencing datasets.
• Length distribution analysis: Computes length distribution of identified eccDNA to characterize structural properties.
• Differential gene enrichment analysis: Performs differential analysis to identify genes enriched with eccDNA.
• Visualization and export: Generates visualizations and publication-quality plots depicting eccDNA structures and analysis results.

Scientific Applications:

• Cancer research: Elucidates the role of eccDNA in tumor biogenesis by analyzing eccDNA content and enriched genes in cancer sequencing data.
• Genetic and regulatory studies: Identifies genes enriched with eccDNA to support studies of genetic variation and regulatory mechanisms.
• Broader eccDNA biology: Enables investigation of eccDNA contributions to other biological processes beyond oncology.

Methodology:

Performs quality control on raw sequencing data, applies algorithms to identify eccDNA from WGS, Circle-seq, and Circulome-seq (short- and long-read), computes length distributions and differential gene enrichment, and generates visualization plots.