Are there any tools that would allow one to count the number of times a kmer is present in both samples of a pair of related Illumina runs? What people usually call tumor/normal or contrast kmer analysis?
I suppose there are plenty of ways to count all possible kmers present in 2 samples from k=1 to k=read length, but fewer that can do this in a reasonable amount of time and disk space.
A minimal output would be: kmer string + count sample 1 + count sample 2
ATGCGGACGCTAGCA 14 1878
ATGCGGACGCTAGC 18 1977
ATGCGGACGCTAGCG 1222 1118