PAN GENOME versus REFERENCE GENOME
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12 weeks ago
Akash D ▴ 40

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!

PAN GENOME ALIGNMENT • 322 views
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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?

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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

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I understand now. Thank you for clarifying this.

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