Extended Data Fig. 6: False duplication examples fixed during manual curation.
From: Towards complete and error-free genome assemblies of all vertebrate species
a, An example of a heterotype duplication in the female zebra finch, non-trio assembly. Left, a self-dot plot of this region generated with Gepard105, with sequences coloured by haplotypes. Gaps, duplicated sequences (green and purple), and haplotype-specific marker densities are indicated at the top. Right, a detailed alignment view of the green haplotype duplication with paternal and maternal markers, self-alignment components, transcripts annotated, contigs, bionano maps, and repeat components displayed in gEVAL95. b, Example of a homotype duplication found in the hummingbird assembly. These were caused by an algorithm bug in FALCON, which was later fixed. c, Example of a combined duplication involving both heterotype (green) and homotype (orange) duplications. Assembly graph structure is shown on the left for clarity, highlighting the overlapping sites at the contig boundary shaded following the duplication type. Assembly errors including the above false duplications were detected and fixed during the curation process.
