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.