I have ~70x PacBio reads and I did an assembly with Canu. I expected a 216 Mb genome but I got a 146Mb assembly of 465 contigs with 1.3G of unassembled data.
I tried to modify some parameters, for overlap length or coverage, but I can't get an assembly which reach the size I wanted (it just increase the number of contigs, or did nothing visible).
Is there any way to improve the size of my assembly by adjusting assembler's parameters, or maybe is there a possible problem with my data? (I didn't polish my data yet, because I have trouble with quiver atm, but I don't expect quiver to up the size of my assembly, am I right?)
What can explain this difference? And what can I do for that?
Thanks for your help!