Heatmap representation of in silico DDH values using different assemblies
in silico DDH (DNA-DNA hybridization) values were estimated using Genome-to-Genome Distance Calculator (GGDC) 2.1 (Nelder & Wedderburn, 1972; Meier-Kolthoff et al., 2013) and the values represented here are calculated according to formula 2 (recommended).
Phylogenetic reconstruction using eight protein-coding gene nucleotide sequences from hybridand Nanopore-only assemblies
Trees were reconstructed using RAxML 8.2.11 (Stamatakis, 2014) with the GTRGAMMA model and 500 bootstrap replications. The final trees were prepared using FigTree v1.4.3 (http://tree.bio.ed.ac.uk/software/figtree/).
Data statistics for the reads used in Vibrio aphrogenes assemblies
Basic information of the data used to assemble V. aphrogenes genome. The genome was sequenced in four different methods; SMRT system from Pacific Biosciences (PacBio), MinION from Oxford Nanopore Technologies (MinION), mate-pair (MiSeq-MP) and paired-end (MiSeq-PE) reads from Illumina MiSeq. For MinION, the data shown here is after debarcoding with Porechop 0.2.2 (https://github.com/rrwick/Porechop) with --untrimmed option.