"Assembly core alignment": Core alignment of de-novo assembled consensus genomes with a global collection of HSV-1 genomes

<i>De novo</i> assembly was performed on the HSV-1 reads using IVA, and contigs were evaluated using the built-in quality tools and with Kraken. to screen for contamination. To analyse our data in a global context, we aligned our <i>de novo</i> assembled contigs along with previously published sequences from around the world to the HSV-1 strain 17 reference genome using parsnp; this restricted the dataset to an alignment of 93,475 common, non-repetitive nucleotide positions including 2,135 parsimony informative sites.