parameters for nanopore Q20 reads

[bernardo1963]

Dear Dr Jue Ruan,
I am using wtdbg2 with the new nanopore Q20 reads. I tried setting -x ccs , but got a very fragmented and incomplete assembly.
May you please suggest which parameters should I try? Should I correct the reads (eg, with Ratatosk) before assembly?
Yours,
Bernardo

[ruanjue]

I haven't tested on nanopore Q20 data. Maybe you need to polish them first, or try -x ont or -x sq.