Pangenome analysis of 882 V. cholerae genomes and detection of clade-specific genes

the synteny-aware pangenome pipeline Panaroo (v1.2.3) was run on the 882 assembled <i>V. cholerae</i> genome set with the option “--clean-mode strict” and default parameters otherwise.<br>To identify clade-specific accessory gene presence/absence patterns, we used custom R scripts (https://github.com/flass/yemenpaper) to compare the the gene presence/absence table output of Panaroo, to the mapped genome tree. Based on lists of genomes assigned to various clades and clusters, we identify accessory genes that are specific of a focus clade in contrast to a background group or a sister clade, considering the contrast significant when the Bonferonni-corrected p-value is below 0.05 and when the frequency of an allele is above 0.8 in the focus clade and below 0.2 in the background clade, or conversely.