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Creating histogram of kmer presence in genomes

Open lucaparmigiani opened this issue 2 years ago • 2 comments

Hi, first of all, thanks for the tool, it is indeed pretty fast and efficient!

I wanted to ask you how to achieve the following:

I have N genomes (assembly). I want to get an histogram of how many kmers appear in 1 Genome, 2 genomes...N genomes. So far I cannot do this, even with kmc_tools, since producing an output with -cs1 will make it not readable for kmc_tools.
If I use -cs > 1 then I cannot apply the union with -ocsum on the two genomes (If I have a kmer appearing twice in the first genome but 0 times in the second genome this will result as if it is present in both).

lucaparmigiani avatar Feb 10 '22 10:02 lucaparmigiani