sometimes the term pan genome and graph genome are used interchangeably, but pan genome can refer to methods that are not specifically graph based. examples of non-graph-based pangenome methods include presence absence variation (PAV) which AFAIK often does not use a graph genome. aligning reads to a graph genome is purported to have less reference bias. non-graph-based pangenomes like PAV analysis may still look at reads also, but it may not align to a graph