Fig. 2

Assembly comparison: long horizonal bars (in greyscale and red) represent contiguous sequences generated by each assembler. The chromosome and plasmids 1 and 2 are coloured according to their overall nucleotide identity when compared to the EC958 reference genome standard (indicated by the scale on the left). Plasmid 3 was only recovered when assembling with Flye and Canu, as indicated. The “other” column refers to contigs that were generated by assemblers but were redundant to the assembly (coloured red). The additional blue horizontal bars in the Canu and Redbean assemblies represent the increased size of the contigs from these assemblers. Contigs that were not reported as circular are marked with a red asterisk(*), while contigs that required manual trimming for circularisation are marked with a blue asterisk. Misassemblies are marked with a red vertical line at their approximate position. The phage tail protein inversion is marked with a blue hourglass