Is there a way to convert long, nanopore reads into illumina paired end reads (not actual illumina reads just simulated reads). In the sense that only the ends of the nanopore reads are retained and these are split into paired end files. I need this sort of thing for a niche subworkflow that takes in distant illumina paired end reads but I only have nanopore reads of this section.
I am assuming it is possible to extract sequences of eg.150bp with a distance corresponding to the insert size you want, one of them would need to be reverse complemented. The question is how much that would help. The error profile, quality scores, and adapter sequences would not be similar. If you just want to test some tools it might be better to make an assembly from the long reads, then use a read simulator to simulate Illumina reads.
Depending on how long your nanopore reads are (think 1 to several kb's) and how many of them, you have you may be able to generate a set of Illumina reads using something like randomreads.sh from BBMap suite. You may need to first convert the reads into fasta format using reformat.sh and then use them as input for the illumina read generation.
As Michael points out this would assume that you are interested in just the sequence and not the error profile of the data you have.
In the sense that only the ends of the nanopore reads are retained and these are split into paired end files.
If that is an absolute requirement you may need to actually write something custom to extract ends.