How should we select the correct kmer size for kmergenie analysis? I have read in wiki page that 'largest k-mer size to consider'. In that case I am looking for valuable comments from you people.
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VineethVenumadhavan •
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.
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Rayan Chikhi
Your explanation seems to be exactly answering my doubt, Rayan Chikhi. I will try this way as well. Thanks a ton.
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Thank you 5heikki
But can you explain a little bit more. Are you saying to run with different k values less than max read length and take an average of them ?
I'm saying you should make assemblies with many different k-mer values and then in the end you merge all the assemblies into one. Also, you obviously can't have larger k-mer values than your read length, I mean, how would you e.g. get a 120-mer from a 90 bp read?
Ok 5heikki. I will try the way you mentioned. Open for more comments if any. thanks a lot