assembly overlapped amplicon data, where to find contained reads

[xiaoli-dong]

I am assembling tilling amplicon data with canu, the amplicon length varies from 500 to 1200 bp. With canu, I can assembly some of the region together to a single contig but there are some other regions failed to assembly although there are a lot of overlapped reads. For those which cannot be unassembled together, there are reads in the unassembled.fasta. I am planning to pick the longest reads from the unassembled file or the longest reads from the contained reads as the represented sequences for the region. Could you give me some hints whether it will make sense? and where I can find the contained reads?