Fig. 1
From: Dark and camouflaged genomic regions remain challenging in CHM13
Dark region analytical workflow. (a) We obtained 20 samples sequenced using Illumina short-reads (100bp and 250bp) and 10 samples sequenced using PacBio and ONT. (b) Using bwa and minimap2 for short and long reads, respectively, we aligned all samples to HG19, HG38 (with and without alternate contigs), and CHM13. (c) We then identified dark and camouflaged regions using our Dark Region Finder. (d) i. Finally, we characterized and quantified dark regions genome wide, along with their differences between references and sequencing platforms. ii. We further assessed how these dark and camouflaged regions affect other short-read based DNA assays (i.e., epigenetic assays). iii. We identified important long-read alignment challenges that need to be addressed. Created with BioRender.com.
