Well, Canu seems to do a reasonable job of assembling long reads for larger organisms but it is laboriously slow!! Trimming and Unitigging stages can take several weeks each. I am now using the reduced list of reads (after mapping to the mitochondrial genome – which reduced reads by ~4%) with the Marvel assembler.
I have been working through the scripts as per the Schmidtea mediterranea example from this recent Nature publication by Grohme et al 2018.
So far so good. However the claim that by using repeat soft masking will reduce computational time by an order of magnitude is yet to be determined. Fingers crossed.