Novel sequence in NGS assemblies compared to the reference assembly. Each assembly was aligned to the Gallus_gallus-2.1 reference using BLAT and unaligned sequence was retained. After contamination removal, the 454/Newbler and Illumina/SOAP assemblies contain 18.9 Mbp and 24.5 Mbp of novel sequence, respectively. The NGS assemblies shared 12.2 Mbp of the non-reference sequence. (a) 454/Newbler (red); (b) Illumina/SOAP (green).