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TGAC / KAT

The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.
http://www.earlham.ac.uk/kat-tools
GNU General Public License v3.0
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How to get two clear peaks? Heterozygous and Homozygous peaks #157

Open hrpelg opened 3 years ago

hrpelg commented 3 years ago

Hi,

I am ploting my ONT long reads against different assemblies using kat comp, using the k=27 by default and I get a plot like this. First peak is not totally clear. I have increased the k to 31 but still see the same. Any suggestions?

image

gonzalogacc commented 3 years ago

Hi hrpelg, the shape of the distribution depends on the quantity/quality of data a lot more than on the k value (for this range of k values). ONT data always produce this kind of "bad" spectras, if you want 2 clear peaks use a high base by base accuracy data type like illumina pe. Best Gonza.-