"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.

本研究采用IVA软件对单纯疱疹病毒1型（Herpes Simplex Virus 1，HSV-1）的测序读段开展从头组装（de novo assembly），并借助内置质量评估工具与克拉肯（Kraken）软件对重叠群（contigs）进行质控以筛查污染序列。为在全球维度下分析本研究数据，我们使用Parsnp工具将本研究获得的从头组装重叠群与此前已发表的全球各地序列比对至HSV-1 17株参考基因组；此次比对将数据集限定为93475个共有的非重复性核苷酸位点的比对集，其中包含2135个简约信息位点。