Can the canu assembler output a fastq file of the final assembly just like HGAP4?
I've created an issue on the Canu github repository for this. I'm not aware of any existing functionality to output FASTQ files, but think that this would be a useful feature to have.

It would be possible to create something like this by aligning the original reads to the genome, generating a pileup from that alignment, then determining the sequence likelihood based on that pileup. Unfortunately, I don't have any scripts that I've written to do that... yet.