BioProject

Nanopore long-read DNA sequencing was performed using standard and ultra-long Nanopore sequencing protocols. For adaptive sequencing, a Nanobind Big DNA Kit (Circulomics) was used to extract uHMW gDNA and an Ultra-Long Sequencing Kit (Oxford Nanopore Technologies, SQK-ULK001) was used for library preparation. The initial processing of raw Nanopore sequencing data (fast5 format) was conducted using Guppy (Oxford Nanopore Technologies) configured to the high-accuracy mode for base-calling. Removal of adapter sequences was achieved through Porechop_ABI v.0.5.0. The distribution of read lengths and base quality across five sequencing runs was evaluated independently using Nanocomp and Nanoplot. Reads with a quality score below 10 (q <10) and a length shorter than 1,000 nucleotides were excluded via Nanofilt 14. The de novo assembly was facilitated by flye v.2.9-b1768 algorithm that is using repeat graphs as a core data structure. Alignment of the de novo MSR repeat assembly (GE_assembly4.0) to the reference mm10 genome was performed using minimap2 v.2.24-r1122 16 to identify MSR contigs containing annotated flanking regions.