title: WGS of Sus scrofa: Large White x Landrace females
design: The short-insert paired-end libraries for the whole-genome sequencing were prepared with a PCR-free protocol using KAPA HyperPrep kit (Roche) with some modifications.  In function of the material availability 0.4-1.0 microgram of genomic DNA was sheared on a Covaris LE220-Plus (Covaris) in order to reach a fragment size of ~400 bp. The fragmented DNA was size-selected for the fragment size of 220-550 bp with AMPure XP beads (Agencourt, Beckman Coulter). The size-selected genomic DNA fragments were end-repaired, adenylated and Illumina platform compatible adaptors with unique dual indexes and unique molecular identifiers (Integrated DNA Technologies) were ligated. The libraries were quality-controlled on an Agilent 2100 Bioanalyzer with the DNA 7500 assay (Agilent) for size and quantified by Kapa Library Quantification Kit for Illumina platforms (Roche). The libraries were sequenced on NovaSeq6000 (Illumina) in paired-end mode with a read length of 2x151+17+8 bp following the manufacturers protocol for dual indexing. Image analysis, base calling and quality scoring of the run were processed using the manufacturers software Real Time Analysis (RTA 3.4.4) and followed by generation of FASTQ sequence files.