Choosing K-mer size in Kmergenie for denovo assembly

Question: Choosing K-mer size in Kmergenie for denovo assembly

5.9 years ago by

India

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.

next-gen assembly genome • 3.5k views

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modified 5.9 years ago by Rayan Chikhi • 1.4k • written 5.9 years ago by VineethVenumadhavan • 30

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 ?

ADD REPLY • link written 5.9 years ago by VineethVenumadhavan • 30

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?

ADD REPLY • link modified 5.9 years ago • written 5.9 years ago by 5heikki ♦ 8.9k

Ok 5heikki. I will try the way you mentioned. Open for more comments if any. thanks a lot

ADD REPLY • link written 5.9 years ago by VineethVenumadhavan • 30

5.9 years ago by

Rayan Chikhi • 1.4k

France, Lille, CNRS

Rayan Chikhi • 1.4k wrote:

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.

ADD COMMENT • link modified 5.9 years ago • written 5.9 years ago by Rayan Chikhi • 1.4k

Your explanation seems to be exactly answering my doubt, Rayan Chikhi. I will try this way as well. Thanks a ton.

ADD REPLY • link written 5.9 years ago by VineethVenumadhavan • 30

5.9 years ago by

5heikki ♦ 8.9k

Finland

5heikki ♦ 8.9k wrote:

Smaller than the length of your reads, larger than 20. Attempt many different values and merge the assemblies in the end.

ADD COMMENT • link written 5.9 years ago by 5heikki ♦ 8.9k

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