parameters for nanopore Q20 reads

ruanjue / wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

GNU General Public License v3.0

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parameters for nanopore Q20 reads #267

Open bernardo1963 opened 2 months ago

bernardo1963 commented 2 months ago

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 commented 2 months ago

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