Is it advisable to include reference genome for pan-genome anlysis when working on specific type strains?

Question

[ThulasiS]

I constructed and analyzed pan-genome but now I got this doubt: Is it advisable to include reference genome for pan-genome analysis when working on specific type strains?

Please suggest me.

Thank you

[Ram]

Your question content is in the title and your body is "Look at the title"? Not a great way to structure your post :-)

I'd recommend moving the content to the body of your post (which I've done for you) and creating an appropriate title to summarize your problem.

[h.mon]

I would go even further: add the info from your comment to Devon to the body of the question, but also explain how you did the analyses.

[ThulasiS]

Thank you Ram Sorry for my format

[Devon Ryan]

Reference genome for whatever the reference strain is?

[ThulasiS]

I didn't get you Devon Ryan. But I'll explain here my concerns. I used Roary pipeline to construct pan-genome. I am anlyzing livestock associated strains but I have reference strain from human origin. So I was thinking if we include reference strain for pangenome size calculation, the size maybe varies. I tried with and without including ref strain but there is not much variation in core genome size. Since it is core. But I was little worried for reviewers questions while presenting the data. So, I was little confused.