PAN GENOME versus REFERENCE GENOME

Question

[SKY]

I have 2 questions.

1) What is the difference between a PAN genome and a REFERENCE genome? 2) Can the PAN genome be a substitute for the REFERENCE genome? Can we use it for the alignment of our reads?

Thanks!

[andres.firrincieli]

Can the PAN genome be a substitute for the REFERENCE genome? Can we use it for the alignment of our reads?

You can do everything but why would you align your reads against a pan-genome?

[cmdcolin]

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

[andres.firrincieli]

I understand now. Thank you for clarifying this.