Removing contaminating sequences
We removed potential contaminating sequences in the draft genome by following the procedure in Jones et al.(Jones et al., 2012). On each scaffold, a 1 Kb fragment without an unknown base “N” was sampled from each 100 Kb window to check for the presence of contaminants. In total we sampled 13,105 one kb fragments and blasted them against the NCBInt database with BLASTN (v. 2.6.0; e-value cut-off= 10-5). Fragments of the BLASTN’ s top hit species that were neither birds nor reptiles were considered contaminants. We extracted contigs that contained these fragments from the scaffolds. In total we found contaminated DNA in 9 scaffolds (153.8 Mb), which included bacteria (N= 2), fishes (N= 1) and mammals (N= 6). Finally, 2,243 scaffolds were retained in the draft black-faced spoonbill genome assembly.