title: Ossabaw minipig 2536
design: Illumina Nextera DNA Flex whole genome sequencing  The DNA was evaluated for its quantity and quality, using Agilent TapeStation 4200 (Santa Clara, CA, USA) and Thermo Fisher Qubit Fluorometer 3.0 (Waltham, MA, USA). One hundred ng high quality genomic DNA of each sample was used for library preparation. Quality of high molecular weight DNA was assessed by gel analysis compared to a ladder of 14 different DNA sizes. Briefly, DNA library was prepared using Illumina Nextera DNA Flex Library Prep Kit (Cat# 20018707; Illumina, Inc. San Diego, CA, USA), following Illumina Nextera DNA Flex Library Prep Reference Guide (Document #1000000025416 v01, April 2018; Illumina, Inc. San Diego, CA, USA). Each resulting library was quantified and its quality accessed by Qubit and Agilent Bioanalyzer (Santa Clara, CA, USA), and multiple libraries were pooled in equal molarity. The pooled library was then denatured, neutralized and sequenced in 150 bp paired-end read format on a NovaSeq 6000 sequencer (Illumina, Inc. San Diego, CA, USA). More than 300 million paired reads per sample were generated for 30-40 fold coverage, and 91% of the sequencing reads reached Q30 (99.9% base call accuracy). A Phred quality score (Q score) was used to measure the quality of sequencing (80x for DNA) {Liao P, Satten GA, Hu YJ. 2017. PhredEM: a phred-score-informed genotype-calling approach for next-generation sequencing studies. Genet. Epidemiol. 41:375-87. DOI: 10.1002/gepi.22048}.