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.
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.
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