How to get the count of each kmer past 255 using khmer
255 is the default maximum size of a Counttable in khmer. You want to do the following:

import khmer
counts = khmer.Counttable(31, 1e7, 1)  # Feel free to change the parameters
counts.set_use_bigcount(True)


The last line increases the maximum value from 255 to 65535. I don't think there's any way to currently go above that without changing the khmer code (at some point you have to increase the size of the number used in the hash table).