"Mapped alignment": multiple alignment consensus genomes obtained by mapping reads on HSV-1 reference strain 17 genome

HSV-1 sequencing reads were extracted from the sequencing data by matching to a BLAST database, mapped to the HSV-1 strain 17 reference genome (NC_001806.2), and variants called at sites with >5 reads coverage using snippy (v3.0), an automated pipeline that parallelises bwa, samtools, and freebayes (v1.0.2) for variant calling; to call consensus SNPs we required >50% of reads in agreement, and reads marked as having secondary mapping to more than one site were discarded before variant calling. We excluded problematic repeat genes (RL1, RL2, RS1) as these contain extensive short sequence repeats (SSRs), which negatively impact upon accurate short-read alignment. This resulted in a final alignment of 138,278 nucleotide positions, of which 2,928 varied between sequences.