Question: Guidelines to choose K-mer size for De bruijn graph based assembly (2nd generation sequencing reads)?
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gravatar for saranpons3
2.8 years ago by
saranpons370
saranpons370 wrote:

Hello members, I would like to know that is there any guidelines to choose K-mer size for Debruijn graph based assembly (2nd generation sequencing reads). I have F.vesca data set in which total number of reads is 12803137 and on an average length of each read is 353 bp. So, I would like to know that what is the best kmer size for assembling these many reads of F.Vesca. Can i try with any k-value above 100 in this case? Thanks.

de bruijn graph k-mer • 1.9k views
ADD COMMENTlink modified 2.8 years ago by h.mon30k • written 2.8 years ago by saranpons370

Which assembler are you considering? Has your data been preprocessed somehow?

ADD REPLYlink written 2.8 years ago by h.mon30k

Dear h.mon, Dataset is not preprocessed already. What should be the k-mer size depends on the assembler? If so, as of now I have velvet installed in my computer.So, i will use velvet assembler.

ADD REPLYlink written 2.8 years ago by saranpons370

The k-mer size is obviously limited by your read lengths, i.e., you cannot have a k-mer that's longer than your read length.

The k-mer size is somewhat independent of the assembler and more to do with your read-lengths, I would imagine. People typically think around the 30-40 range, but with higher k-mers you can achieve a more comprehensive assembled genome (at a computational expense).

ADD REPLYlink written 2.8 years ago by Kevin Blighe61k
1
gravatar for h.mon
2.8 years ago by
h.mon30k
Brazil
h.mon30k wrote:

As you plan to use Velvet: under the folder contrib/, there is the VelvetOptimizer script, it will run Velvet with a range of kmers and select the best assembly for you.

To use Velvet, you have to preprocess your data: remove adapter and low quality regions, and possibly error-correct the reads.

ADD COMMENTlink written 2.8 years ago by h.mon30k

I was also originally going to mention Velvet and VelvetOptimiser.

VelvetOptimiser allows you to test a range of k-mer sizes and it then picks the best based on how you define the following command-line parameters: --optFuncKmer and --optFuncCov

ADD REPLYlink written 2.8 years ago by Kevin Blighe61k
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