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.