Let’s output the first few k-mers and their counts in FASTA format:

For example, this FASTA record:

  >2
  AAGTTTTCA

means the k-mer AAGTTTTCA was seen twice.

To query for a particular k-mer of interest, say ACAGTGGAC, you can use jellyfish query:

This tells us that the ACAGTGGAC k-mer is found in Denge but not Chikungunya.

To get k-mers found in Dengue but not Chikungunya, we can use jellyfish count --if:

The distribution of k-mers now looks different:

This means there are 10,764 k-mers from the Chikungunya genome that were not found in the Dengue genome.