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  • Comparing Kmer distribution between samples

    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.

  • #2
    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.

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    • #3
      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.

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