A Targeted Nanopore Sequencing Pipeline for Tandem Gene Array Engineering

This repository provides a targeted Oxford Nanopore sequencing analysis pipeline for the characterization of tandem gene arrays engineered by gene duplication–based approaches.The pipeline performs barcode-wise processing, including read alignment with minimap2, coverage calculation, extraction of target and flanking sequences, and optional normalization of bedgraph coverage using a .fsa reference genome.It enables quantitative assessment of copy number variation and structural features within tandemly duplicated genomic regions.The workflow is modular, reproducible, and controlled via command-line arguments and environment variables, allowing flexible adaptation to different experimental designs.This pipeline is intended to support genome engineering, synthetic biology, and functional genomics studies involving tandem gene array manipulation.