title: 14X WGS of USMARC Beef Diversity Panel version 2.9
design: DNA was extracted from commercial semen with a typical phenol:chloroform method and stored at 4C in 10 mM TrisCl, 1 mM EDTA (pH 8.0).  Approximately 5 _g of bovine genomic DNA was fragmented by focused-ultrasonication to generate fragments less than 800 bp long (Covaris, Inc. Woburn, Massachusetts USA).  These fragments were used to make an indexed, 500 bp paired-end library according to the manufacturerÕs instructions (TruSeq DNA PCR-Free LT Library Preparation Kits A and B, Illumina, Inc., San Diego, California USA).  After construction, indexed libraries were pooled in groups of four to eight, and sequenced with a massively parallel sequencing machine and high-output kits (NextSeq500, two by 150 paired-end reads, Illumina Inc.).  After sequencing, the raw reads were filtered to remove adaptor sequences, contaminating dimer sequences, and low quality reads.  Pooled libraries with compatible indexes were repeatedly sequenced until 40 GBb of data with greater than Q20 quality, was collected for each sire.