[khmer] Counting kmers and disabling reverse complement

Lester Mackey lmackey at stanford.edu
Fri Jun 14 00:22:19 PDT 2013


Dear khmer Discussion List,

If my goal is to obtain a vector of kmer counts quickly from a FASTA or
FASTQ file, is there any reason to prefer ktable to one of your other data
structures, like the counting hash table?

I've noticed that ktable hashes a kmer and its reverse complement to the
same bin.  Is there an easy way to disable this feature (and thereby count
each kmer and reverse complement separately)?

Thanks,
Lester
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