Any tools to count kmers in tumor/normal (contrast) pairs of samples?

Question

[14134125465346445]

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
...

Answer 1

[Sean Davis]

A short list of kmer counting software is available here:

http://www.homolog.us/Tutorials/index.php?p=3.7&s=2