title: ddRAD sequencing of Gir_96_16
design: Genomic DNA of each cultivar was double digested and incubated at 37C for 1620h. Fragmented DNA was then purified with AMPureXP beads (Agencourt) and ligated to barcoded adapters. Samples were pooled on multiplexing batches and bead purified. For each pool, targeted fragments distribution was collected on a BluePippin instrument (Sage Science Inc.). The gel eluted fraction was amplified with oligo primers that introduced TruSeq indexes and subsequently bead purified. The resulting libraries were checked with both Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and Bioanalyzer DNA assay (Agilent Technologies, Santa Clara, CA). Libraries were finally processed with Illumina NovaSeq 6000 platform with paired end chemistry.