Question: kmer for sample list
0
gravatar for ARich
2.0 years ago by
ARich60
United States
ARich60 wrote:

Dear All,

I am working with paired end metagenomic illumina data. 

I need to know that on providing list file with multiple sample entries does kmergenie decide kmer for all the samples provide in the list or how it treats the sample list?

I means for metagenomic assembly is feasible to have one kmer for all samples or do you recommend to run kmergenie with all the samples separately.

Thanks

Best,

AR

kmergenie • 791 views
ADD COMMENTlink modified 21 months ago • written 2.0 years ago by ARich60
0
gravatar for Rayan Chikhi
2.0 years ago by
Rayan Chikhi1.2k
France, Lille, CNRS
Rayan Chikhi1.2k wrote:

Hi,

 

Kmergenie most likely won't work for metagenomic data, I'm sorry. It expects a single genome. Hence, if your data contains more than one genome, it is quite likely that it won't work. (the model won't be able to fit the kmer histograms that have been generated.)

If you have separate samples and each sample contains a single genome, then it is recommended to run kmergenie on samples separately. However, if each sample contains multiple genomes, then kmergenie most likely won't work.

 

The good news is that for metagenomics assembly, you could try multi-k assemblers, where you do not need to specify a best k value: SPAdes or Megahit.

ADD COMMENTlink written 2.0 years ago by Rayan Chikhi1.2k
0
gravatar for ARich
21 months ago by
ARich60
United States
ARich60 wrote:

Dear Rayan,

Thanks Yes i tested it with Spaded it does have metagenomic option optimizing to the best kmer.

ADD COMMENTlink written 21 months ago by ARich60
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