title: Illumina HiSeq 2500 sequencing of Himantopus himantopus
design: Paired-end libraries for the pied stilt were prepared at the University of Otago using the Illumina TruSeq DNA PCR-free protocol according to manufacturer specifications, with genomic DNA fragmented to 350 bp. End repair and adapter ligation for sequence barcoding were carried out and libraries were indexed with unique 6 bp sequences. Sequencing of pied stilt libraries was completed by New Zealand Genomics Limited (NZGL), where sample libraries were pooled with four other samples and spread across five lanes of a flow cell for 2 x 125 bp sequencing on an Illumina HiSeq 2500.