Question: What are the parameters in IMG output?

[martinastoycheva]

Hello,

I wanted to use the IMG helper script you provide for estimating the size of the pangenome to avoid the common errors assosiated with simply plotting a rarefaction curve. However, I am not familiar with this type of models and the paper you cite for it seems rather complicated and mathsy so I was wondering if you could give a brief explanation of the parameters that the model estmates. I assume ess is the estikate for the core genome size but what do v1, v2 and u1 mean?

Thanks very much!
Martina

[gtonkinhill]

Hi,

I have found that this version of the IMG model does not perform particularly well and would now recommend the panstripe method available here.

If you are keen to use the IMG model the implementation in panicmage tends to outperform that of Collins et al.