Question about ambiguous k-mers with ambiguous nucleotides about mash HOT 3 OPEN

They are indeed thrown out; by default only k-mers with ACGT are used.

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Thanks for the quick reply. Sounds like this is handled correctly. My only complaint is that it is not documented clearly here or in the paper. Perhaps this could be noted to the help or documentation. Even more obvious to the user would be to note the number of dropped kmers in with the info.

from mash.

A quick note on this. I also had this question upon reading the paper. I found this, http://mash.readthedocs.io/en/latest/sketches.html#strand-and-alphabet, though still left me with the question of how gaps/ambiguous characters would be handled. My recommendation would be for http://mash.readthedocs.io/en/latest/sketches.html#ambiguous-characters section directly after #strand-and-alphabet.

Thanks for all your work on this by the way! This is a great tool.

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