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. 2021 Apr 29;22:120. doi: 10.1186/s13059-021-02336-9

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© The Author(s) 2021

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. 1 — Paired comparisons of mitoVGP assemblies with NOVOPlasty and Genbank/RefSeq assemblies. NOVOPlasty assemblies are split into three categories: (1) circular (green), (2) single-contig (yellow), (3) multiple-contigs (orange). a–d Comparisons between NOVOPlasty and mitoVGP assemblies for sequence identity (a, including and excluding IUPAC bases), assembly length (b), annotated repeat length (c, in circular NOVOPlasty assemblies and matched mitoVGP assemblies), and number of gene duplications (d, in circular NOVOPlasty assemblies and matched mitoVGP assemblies). Note that in panel a, single-contig assemblies show levels of identity very similar to circular ones, and therefore they largely overlap and are difficult to distinguish from the figure. e–h Genbank/RefSeq comparisons of mitogenome assembly length (e), annotated repeat length (f), number of missing genes (g), and number of gene duplications (h). Statistical significance (one-sided paired samples Wilcoxon test) is reported above each plot. In the first plot, outliers having identity < 99.7% are labeled. Top10 outliers in the 20th and 80th percentiles are labeled in the other plots