KaryoExplorer: An Automated Digital Karyotyping Pipeline with Interactive Visualizations

Induced pluripotent stem cells (iPSCs) are generated for a wide variety of experiments and applications (Takahashi & Yamanaka, 2006, 2007). To ensure high quality of the generated iPSCs a routine quality control (QC) is performed including screening for copy number variation (CNV) and loss of heterozygosity (LoH). Researchers often have to use multiple tools, manual file handling, and static plots to interpret the results (Hussein & others, 2011; Laurent &15 others, 2011; Mayshar & others, 2010). KaryoExplorer is a Nextflow-based computational pipeline that performs CNV and LoH analysis on Illumina genotyping arrays and provides a single, self-contained and interactive HyperText Markup Language (HTML) report (Di Tommaso & others, 2017). It integrates CNV calls (deletions/duplications) and runs of homozygosity (ROH) to surface candidate copy-neutral LoH (cnLoH). The HTML report presents synchronized B-allele frequency (BAF), log-R ratio (LRR), and copy number (CN) visualizations enabling investigation on base level for each chromosome in addition to genome-wide karyotype maps and QC summaries. The report can be accessed using a web browser without the need for any additional software.