SRX3872563 HGM_200 SRP136936 PRJNA257563 Ion Proton shotgun sequencing for library preparation clean genomic DNA (aprox. 1000 ng) were fragmented by 200-300 bp using Covaris S220 System (Covaris, Woburn, Massachusetts, USA). After that, Ion Xpress Plus Fragment Library Kit (Life Technologies) was employed for barcode shotgun-library sample preparation. Emulsion PCR was performed using the One Touch system (Life Technologies). Beads were prepared using the One Touch 2 and Template Kit v2 Sequencing was performed by using Ion Proton 200 sequencing kit v2 on the P1 Ion chip. Raw data has been uploaded to NCBI SRA database SRS3113988 SAMN06018827 HGM_200 WGS GENOMIC unspecified Ion Torrent Proton SRX3872564 HGM_56 SRP136936 PRJNA257563 Ion Torrent mate-pair sequencing - mate-pair library with 3-6Kb fragment was prepared from a sample genomic DNA with reagent kits Ion TrueMate Library Reagents (Life Technologies). To conduct emulsion PCR, the Ion PGM template OT2 400 kit (Life Technologies) was utilised. Sequencing was performed in accordance with manufacturer protocol for the genome analyser Ion Torrent PGM (Life Technologies) using an Ion 318 chip and Ion PGM sequencing 400 kit v2 (Life Technologies). For separation non-mate reads and spliting true mate reads we use script matePairingSplitReads.py SRS3113988 SAMN06018827 HGM_56 WGS GENOMIC unspecified Ion Torrent PGM SRX3872565 HGM_812 SRP136936 PRJNA257563 Illumina mate-pair sequencing - mate-pair library with 8-12Kb fragment was prepared from a sample genomic DNA with reagent kits Nextera Mate Pair library Sample Prep kit (Illumina) and TruSeq DNA Sample Prep kit (Illumina) in the protocols, recommended by the manufacturer. Sample was sequenced on the MiSeq platform (Illumina) using a 2 150 cycle MiSeq V2 reagent kit, following standard Illumina sequencing protocols. Demultiplexing was performed using bcl2fastq v2.17.1.14 Conversion Software (Illumina). Adaptor sequences were removed from reads during demultiplexing. For trimming and separation of single-end, paired-end, mate-pair reads we used NxTrim SRS3113988 SAMN06018827 HGM_812 WGS GENOMIC unspecified Illumina MiSeq