K-mer comparison density plot

[dirkjanvw]

Hi, thanks for providing an amazing tool! It works exactly as I expected!

I especially see the benefits of using merqury over KAT with regard to speed. However, with KAT, I am able to create density plots of the comparisons of two sets of k-mers (kat plot density). I know that this does not make sense when calculating the completeness of a genome assembly, but I was wondering: is it possible to use merqury (or meryl?) to create these density plots for a comparison of two meryl databases?

[arangrhie]

Hello @dirkjanvw,

You could try using to_hist_for_plotting.sh for your meryl dbs. For example,

sh $MERQURY/plot/to_hist_for_plotting.sh db1.meryl DB1 db2.meryl DB2 > db1_and_db2.hist

This generates one histogram file that could be fed into the plot_spectra_cn.R. The color code wouldn't be that fancy and follows the ones used in Merqury, but you would be able to plot whatever meryl db has in it and compare.

Rscript $MERQURY/plot/plot_spectra_cn.R --help

has the detailed options you can adjust for plotting.

[dirkjanvw]

Thanks a lot for the reply! I haven't manage to create 2d density plots, but the spectra-cn plots are actually way more useful for my purposes of comparing sequencing libraries. The scripts work perfectly!