Comparing Kmer distribution between samples

[jgibbons1]

Hi all,

I am sequencing 2 genomes which are identical, with the exception of one chromosome (Y chromosome). The Y is highly repetitive though and will not assemble well.

To get an proxy of what sort of motifs are on the Y, I want to compare Kmer distribution between samples with the idea being that the outlier kmers will consist of the Y-chromosome.

If anyone has tried something like this before I would be very interested in hearing how. Are specific kmer counting software better than others?

Any thoughts would be greatly appreciated.

[Thowell]

I am doing a similar project, and am curious what you ended up doing for your project. I am thinking of using jellyfish for counting the kmers.

[jgibbons1]

Hi Thowell,

I ended up using jellyfish and then used a custom perl script to compare kmer counts between samples. It seemed to work fairly well.