Benchmarking of PacBio HiFi and Oxford Nanopore Sequencing

This repository provides the analysis code for the study:

Benchmarking PacBio HiFi and Oxford Nanopore Long-Read Sequencing for Variant Detection, Phasing, Assembly, and Methylation in Family Trios

Repository Structure

Long-read-WGS/
├── 01_SequencingMetrics     # Yield, read length, and quality metrics
├── 02_SNV                   # Small variant analysis
├── 03_SV                    # Structural variant analysis
├── 04_TR                    # Tandem-repeat analysis
├── 05_Methylation           # Methylation analysis
├── 06_Phasing               # Phasing analysis
├── 07_HLAtyping             # HLA allele concordance analysis
└── README.md