Question: Choosing K-mer size in Kmergenie for denovo assembly
2
gravatar for VineethVenumadhavan
3.2 years ago by
India
VineethVenumadhavan30 wrote:

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 • 2.4k views
ADD COMMENTlink modified 3.1 years ago by Rayan Chikhi1.2k • written 3.2 years ago by VineethVenumadhavan30

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 REPLYlink written 3.2 years ago by VineethVenumadhavan30

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 REPLYlink modified 3.2 years ago • written 3.2 years ago by 5heikki6.7k

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

ADD REPLYlink written 3.1 years ago by VineethVenumadhavan30
3
gravatar for Rayan Chikhi
3.1 years ago by
Rayan Chikhi1.2k
France, Lille, CNRS
Rayan Chikhi1.2k 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 COMMENTlink modified 3.1 years ago • written 3.1 years ago by Rayan Chikhi1.2k
1

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

ADD REPLYlink written 3.1 years ago by VineethVenumadhavan30
2
gravatar for 5heikki
3.2 years ago by
5heikki6.7k
Finland
5heikki6.7k wrote:

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

ADD COMMENTlink written 3.2 years ago by 5heikki6.7k
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