Difference between reading concatenated PE reads and merging paired end .jf outputs independently

[JWrighty97]

I have been finding my way through kmer counting some illumina paired end read sequence data for my PhD (10 files, 5 samples). When putting the data through jellyfish I have found massive difference between the outcomes after further downstream analysis i.e GenomeScope.

Attached is the images of the downstream analysis with concatenating a library (four files) before going through jellyfish and using jellyfish merge to merge the .jf outputs of each file independently.

Is this how you would recommend using your software?

Best wishes,