Bulk Hi-C Module (chr3d.hic)
Complete Hi-C processing pipeline for bulk (population-level) chromatin interaction data.
All classes in this module can be imported either from chr3d directly or from chr3d.hic.
Overview
The bulk Hi-C module provides a complete pipeline for processing population-level Hi-C data, from raw FASTQ files to contact matrices and downstream analysis.
Components
Pipeline Orchestrator
- HiCPipeline - Complete Hi-C pipeline orchestrator
Individual Processing Steps
- HiCAligner - BWA MEM alignment for Hi-C data
- HiCSamProcessor - SAM/BAM processing with samtools
- HiCPairsProcessor - Pairtools for pairs processing
- HiCMatrixGenerator - Cooler for contact matrix generation
Utilities
- HiCQCAnalyzer - Quality control analyzer
- FastqSplitter - Split FASTQ files for parallel processing
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