Hi @zwei,
JoinedSequencesWithQuality reads will be treated like SequencesWithQuality. Joined reads have already been joined into single reads so from a human perspective we can consider these to be single-end reads (that’s what they’d look like if we export the artifact). From a machine perspective we apply the semantic type to ensure that these data are only used in an appropriate manner, so for example we cannot input JoinedSequencesWithQuality to dada2, which requires unadulterated single/paired-end reads.
You can read more about joining reads (and then denoising with deblur) here.
I hope that helps!