Are there any functions in the bioconductor packages that merge Illumina paired end reads, similar to FLASH or PEAR? I assumed this would be a function in ShortReads but couldn't find anything about this in the documentation. Thanks.

This is not possible in ShortRead; I do not know of an implementation in Bioconductor.

It looks like the Rfastp package has explicit support for this. I'm testing it out now, so not sure how well it works yet.