ML tree of 33 mapped V. cholerae Clade D genomes

Maximum-likelihood phylogeny of the 33 mapped V. cholerae Clade D (including ST555) genomes.
For variant calling, Illumina short reads were mapped against the novel reference strain CNRVC190247 genome. We mapped all 21 short read sets from 2018-2019 Yemeni V. cholerae isolates, provided read mapping were mapped at a sufficient depth (see below); we also mapped read sets from 12 contextual V. cholerae isolates linked to ST555. Reads were trimmed with Trimmomatic, mapped to both CNRVC190247 reference chromosomes with BWA-MEM. All mapped genomes had an average read depth above 5x over the two chromosomes and were deemed of sufficient read depth for analysis. We used the software suite samtools/bcftools v1.9 to call variants with a minimum coverage of 10x read depth, excluding indels. Resulting consensus sequences were combined and processed with snp-sites (Page et al., 2016) to produce a single nucleotide polymorphism (SNP) alignment featuring 91,312 positions.