search

marschall-lab / panacus

Panacus is a tool for computing statistics for GFA-formatted pangenome graphs
MIT License
73 stars 4 forks source link

What is the meaning of common and consensus? #1

Closed Orz-CQ closed 1 year ago

Orz-CQ commented 2 years ago

Hi,

Thanks for this approach to check the GFA file's growth plot. But I am curious the meaning of "common" and "consensus". Which means the number that all accessions contained? I guess "common". What about "consensus"?

Best wishes, Lan

danydoerr commented 2 years ago

Hi Lan,

admittedly, these labels have been chosen somewhat arbitrarily. "Common" means that the corresponding node/base pair/edge appears in all accessions, whereas consensus counts those appearing in >=50%.

We are working on an entirely revised version that will be released soon where these labels can be set by the user.

-dany

Orz-CQ commented 2 years ago

Hi dany,

Thanks for your soon reply.

I have one more question. Here, in the plot, least-squares fit to m*X^ (m=20331763.197, γ=0.811). What can we get from this number? Such as what the meaning of the higher m or higher γ?

Many thanks! Lan

danydoerr commented 2 years ago

Typically, only the γ factor is of interest, it indicates wheather the pangenome is open or closed. γ takes on values between 0 and 1, those closer to 0 indicate a close pangenome, whereas those closer to 1 indicate an open pangenome. More details can be found here: https://doi.org/10.1016/j.mib.2008.09.006

Orz-CQ commented 2 years ago

Got it. Thanks!