<p>How should we select the correct kmer size for kmergenie analysis? I have read in wiki page that &#39;largest k-mer size to consider&#39;. In that case I am looking for valuable comments from you people.</p>

There may be a misunderstanding here.

"Selecting the correct kmer size for kmergenie analysis" implies that kmergenie would perhaps require user assistance?

This is precisely the opposite, it is designed to choose k for you. Just run kmergenie without any parameter, and it will explicitly print what it thinks is a good kmer size. Most of the time, the value is accurate.

Additionally, for unusual cases, you can take a look at the generated HTML report to make a more informed decision.