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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. 6 — Evaluating haplotype completeness for diploid assemblies using Merqury. Spectra-cn plots of the maternal and paternal assemblies of the TrioCanu NA12878 assembly are displayed as a confusion matrix. a Hap-mer spectra-cn plot of the maternal assembly. All maternal hap-mers are expected to be found in the maternal (top left), with no paternal hap-mers (top right). Any maternal hap-mers not found in this assembly are missing hap-mers (top left, black). Paternal hap-mers (top right, red) are false positive phasing errors. b Hap-mer spectra-cn plot of the paternal assembly. This time, no maternal hap-mers should be seen (bottom left), and only paternal markers are expected to be present (bottom right). TP, true positives; FN, false negatives; TN, true negatives; FP, false positives