I'm looking for some software that can "efficiently" (time and memory) compute the exact percentage of non-unique k-mers in a genome for given k. I don't need the k-mers or the abundances itself, I just need the percentage.
Alternatively, the result could be:
- the number of different k-mers observed in the genome
- the number of unique k-mers, i.e. k-mers that occur only once in the genome, or the number of non-unique k-mers, i.e., k-mers that occur more than once in the genome.
which can be easily used to compute the requested percentage.
- don't count k-mers with ambiguous nucleotides
- count a k-mer and its reverse complement together
- k upto 50 or 100
- for large genomes (upto some GB)
For the study in mind, I like to vary k. Hence, I will run the software several times with different k.
Any help is welcome.