title: ddradseq
design: ddRAD libraries are produced using an IGATech custom protocol, with minor modifications with respect to Peterson et al. 2012 (Peterson et al. 2012). To select the best combination of the two restriction enzymes, an in silico analysis on the reference genome of a closely related species (ifavailable) is performed. Selected enzymes are SphI-HindIII. GenomicDNA is fluorimetrically quantified, normalized to a uniform concentration and double digested.Fragmented DNA is purified with AMPureXP beads (Agencourt) and ligated to barcoded adapters. Samples are pooled on multiplexing batches and bead purified. For each pool, targeted fragments distribution is collected on BluePippin instrument (Sage Science Inc.). Geleluted fraction is amplified with oligo primers that introduce TruSeq indexes and subsequently bead purified. The resulting libraries are checked with both Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and Bioanalyzer DNA assay (Agilent technologies, Santa Clara, CA). Libraries are processed with Illumina cBot for cluster generation on the flowcell, following the manufacturers instructions and sequenced with V4 chemistry paired end 125bp mode onHiSeq2500 instrument (Illumina, San Diego, CA).