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

I have been finding my way through kmer counting some illumina paired end read sequence data for my PhD. 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) Library reads merged before going through JF before going through jellyfish and using jellyfish merge to merge the .jf outputs of each file independently Library reads after each file went through individual kmer counting and then jellyfish merge.

The library consists of 288.4m 150bp reads all trimmed to Q25.

Is this merging the .jf outputs the best way to use the software?

Best wishes,

jellyfish kmer genomescope
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written by joshua.j.wright • joshua.j.wright

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