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. 2020 Sep 14;21:245. doi: 10.1186/s13059-020-02134-9

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© The Author(s) 2020

Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 2 — Merqury assembly spectrum plots for evaluating k-mer completeness. K-mers are colored by their presence in the reads and primary/alternate assemblies. a Distinct k-mer assembly spectrum (spectra-asm) plot of both TrioCanu Col and Cvi haplotype assemblies. This plot shows the assembly-specific (red and blue) and shared portion of k-mers (green). b Spectra-asm plot of the FALCON-Unzip assembly. The primary assembly has more k-mers (red) compared to the alternate assembly (blue). c Spectra-asm plot of the Canu assembly which is a mixture of both haplotypes. A small fraction of 1-copy k-mers is found only in the reads (black peak around 12~30×), which represents heterozygous variants missing from the assembly