KaryoExplorer: an automated digital karyotyping pipeline with interactive visualizations

Abstract

Routine genomic quality control (QC) is essential for ensuring the integrity of induced pluripotent stem cells used in disease modeling, regenerative medicine, and related cell line applications. However, digital karyotyping workflows based on single nucleotide polymorphism genotyping arrays are often fragmented, requiring separate tools for copy number variation (CNV) detection, loss of heterozygosity (LOH) analysis, and result visualization. This fragmentation complicates interpretation, limits reproducibility, and creates practical barriers for routine use and collaborative review. Here, we present KaryoExplorer, an automated Nextflow-based pipeline for digital karyotyping of genotyping array data that generates an easy-to-use, self-contained interactive HTML report. CNV calling and runs of homozygosity (ROH)-based detection of candidate copy-neutral loss of heterozygosity (cnLOH) regions are integrated into a unified, reproducible workflow. The resulting browser-based report combines genome-wide karyograms, chromosome-level B-allele frequency (BAF), log-R ratio (LRR), copy number (CN) tracks, QC summaries, event tables, and synchronized interactive views that support intuitive navigation from sample overview to signal-level inspection. Validation on a 36-sample genotyping dataset, evaluated in both single-sample and paired analysis modes, showed that deletion events ($\mathrm{CN} \leq 1$) overlapped ROH segments with a median of 99.2%, supporting the biological consistency of the integration strategy. Candidate cnLOH regions defined by ROH overlapping diploid copy number states ($\mathrm{CN}=2$) showed increased BAF deviation relative to diploid non-ROH regions, and were highly reproducible across paired technical replicates. KaryoExplorer therefore streamlines digital karyotyping by coupling automated analysis with accessible, interactive, and shareable reporting for genomic QC workflows.