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. 2021 Jun 25;22:474. doi: 10.1186/s12864-021-07767-z

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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. 5 — ST131 Phylogeny to assess quality of ONT assemblies: A Phylogenetic tree created using assemblies generated with MicroPIPE v0.8 (Guppy v3.4.3) and other ST131 genomes for context [17]. Branches are coloured based on the ST131 clade they belong to, as per [17] (Red = clade A, Orange = clade B, Green = clade C). dark blue: Complete polished assemblies from the MicroPIPE pipeline next to their Illumina assembly counterpart in the tree, light blue: assemblies with incomplete polishing (i.e. Illumina only, Nanopore only or no polishing) clustered with their Illumina counterpart, red: discrepant clustering of Nanopore assemblies. B Phylogenetic tree created using assemblies generated with MicroPIPE v0.9 (Guppy v3.6.1). Annotations are same as in A. C Position of alternative (alt) and reference (ref) alleles compared to the EC958 reference standard chromosome present on branch leading to discrepant ONT assemblies as indicated by the star in (A)