Question: best kmer for genome size estimation
0
gravatar for popayekid55
5 days ago by
popayekid5530
popayekid5530 wrote:

Hi,

How do i select a best kmer for genome size estimation using jellyfish. I did using 31 and 41 both gave me a different result. Read chemistry is 150*2. are there any other tools, i am trying gce also.

Thanks in advance

kmer genome • 130 views
ADD COMMENTlink modified 3 days ago • written 5 days ago by popayekid5530
1
gravatar for toralmanvar
5 days ago by
toralmanvar40
toralmanvar40 wrote:

Hello,

You can give a try to kmergenie.

Mostly it works for me.

ADD COMMENTlink written 5 days ago by toralmanvar40

I have tried that and best kmer from kmergenie was way too high. For this data it was 119. I was not sure this kmer to use in jellyfish for genome estimation

ADD REPLYlink written 4 days ago by popayekid5530

I don't understand when kmergenie along with best kmer already gives you estimated genome size then why you want to use jellyfish again for the same? Checking the histo.pdf file generated from kmergenie properly can give you required answer.

ADD REPLYlink written 4 days ago by toralmanvar40
1
gravatar for genomax
4 days ago by
genomax39k
United States
genomax39k wrote:

You can use Jellyfish as described here. BBMap suite has kmercountexact.sh that can be used for this purpose.

ADD COMMENTlink written 4 days ago by genomax39k

Thank you for the response. I was following the 1st link for genome estimation. It was mentioned for eukaryote 17-31 would be fine in jellyfish. In the tutorial they chose 25. Still not understanding how to choose the kmer length for counting. kmercountexact.sh is taking kmer length of 31 as default.

Is 31 a std kmer length for any eukaryote genomes?

ADD REPLYlink written 4 days ago by popayekid5530
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