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. 2021 Apr 28;592(7856):737–746. doi: 10.1038/s41586-021-03451-0

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© The Author(s) 2021

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 6 — 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.