Dedupe and nanopore amplicon reads

[anitagh]

I'd like to use dedupe.sh to remove contained amplicon Nanopore reads and haven't had much success. My reads are about 4-5Kb and I have tried the following combinations.

minidentity=90 e=10
minidentity=80 e=10
minidentity=70 e=10
minidentity=70 e=20

I observe 0 containments and only 2 overlaps. Am I missing a parameter?

Many Thanks,
Azita