Recommendation on k-mer counting package for multiple libraries?

Question

[johnnytam100]

I want to count all the 30-mers (or partially e.g. every 30-mer starting with "A") in multiple libraries to produce a k-mer abundance table partly like this :

kmer lib1 lib2 lib3 lib4 lib5
AAAAAAAAAAAAAAAAAAAAAAAAAGAGAA 0 0 2 6 4
AAAAAAAAAAAAAAAAAAAAAAAAAGATCT 0 1 1 0 2
AAAAAAAAAAAAAAAAAAAAAAAAAGGAAA 0 1 1 5 0
AAAAAAAAAAAAAAAAAAAAAAAAAGGAAG 1 0 0 0 5
AAAAAAAAAAAAAAAAAAAAAAAAAGGAGG 0 0 1 0 1

Any recommendation on what package to use on a linux system?

Thank you!

Answer 1

[5heikki]

I use Jellyfish 2 for k-mer counting.