Detection Workflow

This page describes the complete workflow of the circDNA detection pipeline, showing how the different detection methods work together to identify circular DNA elements.

Pipeline Overview

The circDNA detection pipeline consists of four main phases that work together to provide comprehensive circular DNA detection:

graph TD A[Input BAM File] --> B[Coverage Pattern Analysis] A --> C[Junction Detection] A --> D[Split-Read Analysis] B --> E[Coverage Candidates] C --> F[Junction Candidates] D --> G[Split-Read Candidates] E --> H[Multi-Modal Integration] F --> H G --> H H --> I[Confidence Scoring] I --> J[Output Filtering] J --> K[BED Format Output] style A fill:#e1f5fe style K fill:#e8f5e8 style H fill:#fff3e0

Detailed Workflow

Phase 1: Coverage Pattern Analysis

graph LR A[BAM Input] --> B[Calculate Coverage Depth] B --> C[Identify Enriched Regions] C --> D[Apply Fold Enrichment Threshold] D --> E[Coverage Candidates] style A fill:#e1f5fe style E fill:#e8f5e8

Purpose: Identifies regions with elevated coverage patterns characteristic of circular DNA elements.

Process: 1. Calculate coverage depth across all genomic regions 2. Identify regions with significantly elevated coverage 3. Apply minimum fold enrichment threshold (default: 1.5x) 4. Filter by minimum coverage depth (default: 5x)

Phase 2: Junction Detection

graph LR A[BAM Input] --> B[Identify Split Alignments] B --> C[Find Back-to-Back Junctions] C --> D[Validate Junction Signatures] D --> E[Junction Candidates] style A fill:#e1f5fe style E fill:#e8f5e8

Purpose: Detects back-to-back junction signatures at circular DNA breakpoints.

Process: 1. Identify reads with split alignments 2. Look for back-to-back junction patterns 3. Validate junction signatures for circular characteristics 4. Filter by junction quality and support

Phase 3: Split-Read Analysis

graph LR A[BAM Input] --> B[Extract Split Reads] B --> C[Analyze Alignment Patterns] C --> D[Identify Circular Signatures] D --> E[Split-Read Candidates] style A fill:#e1f5fe style E fill:#e8f5e8

Purpose: Analyzes split alignments for signatures consistent with circular DNA structures.

Process: 1. Extract reads with split alignments 2. Analyze alignment patterns for circular signatures 3. Identify reads supporting circular structures 4. Validate split-read evidence

Phase 4: Multi-Modal Integration

graph TD A[Coverage Candidates] --> D[Evidence Integration] B[Junction Candidates] --> D C[Split-Read Candidates] --> D D --> E[Confidence Scoring] E --> F[Threshold Filtering] F --> G[Final Candidates] style D fill:#fff3e0 style G fill:#e8f5e8

Purpose: Combines evidence from all detection methods and assigns confidence scores.

Process: 1. Integrate candidates from all detection methods 2. Calculate multi-evidence confidence scores 3. Apply final filtering thresholds 4. Generate final candidate list

Parameter Configuration

The workflow can be customized through various parameters:

Parameter Default Description
min_fold_enrichment 1.5 Minimum fold enrichment for coverage detection
min_coverage 5 Minimum coverage depth
min_length 200 Minimum circular DNA length
max_length 100000 Maximum circular DNA length

Output Generation

The final step generates results in BED format with additional columns:

  • Standard BED columns (chr, start, end, name, score, strand)
  • Detection method information
  • Confidence scores
  • Supporting evidence details

Quality Control

Throughout the pipeline, multiple quality control measures ensure reliable detection:

  • Coverage validation: Ensures sufficient read support
  • Junction validation: Confirms genuine circular junction signatures
  • Split-read validation: Validates split-read evidence quality
  • Multi-modal consensus: Requires evidence from multiple detection methods for high-confidence calls