Sketching paired- and single-end reads together

[VGalata]

Hello,

I have a question about how to process a sample if it has paired- but also single-end reads: my samples have FASTQ files with paired reads (R1 and R2) and a FASTQ files with single-end reads only (SE), and I would like to compute pair-wise dissimilarity between all the samples in my dataset.

What would be the best strategy to do that? I wanted to concatenate R1, R2 and SE per sample to compute the sketches but I am not sure if this would be the recommended way.

Thanks in advance!

Best,
Valentina