Fig. 5
From: MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction
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)