A Bioinformatics Workflow to Identify eccDNA Using ECCFP From Long-Read Nanopore Sequencing Data.

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Extrachromosomal circular DNA (eccDNA) plays a role in gene regulation, but its detection is challenging.
• Existing bioinformatics pipelines for eccDNA analysis often lack accuracy and efficiency.
• Small eccDNAs are particularly important for gene regulation.

Purpose of the Study:

• To introduce a novel bioinformatics pipeline, ECCFP, for accurate eccDNA identification from long-read Nanopore sequencing data.
• To provide a user-friendly protocol for eccDNA analysis, accessible to researchers without extensive bioinformatics experience.
• To improve the sensitivity, accuracy, and efficiency of eccDNA detection compared to existing methods.

Main Methods:

• Development of the EccDNA Caller based on Consecutive Full Pass (ECCFP) pipeline.
• Integration of raw data quality control, adapter/barcode trimming, and alignment to a reference genome.
• Application of ECCFP to Nanopore sequencing data for eccDNA identification.

Main Results:

• ECCFP demonstrates significantly improved detection sensitivity and accuracy for eccDNA.
• The pipeline offers enhanced runtime efficiency compared to other existing tools.
• Detailed results include accurate eccDNA positioning, consensus sequences, and variant identification.

Conclusions:

• ECCFP provides a robust and efficient solution for identifying eccDNA from Nanopore sequencing data.
• The pipeline lowers the barrier to entry for eccDNA research, enabling broader application.
• ECCFP offers a high-efficiency, low-false-positive rate tool for eccDNA analysis.