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Old 05-21-2019, 01:13 PM   #3
SNPsaurus
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Location: Eugene, OR

Join Date: May 2013
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wtdbg2 will overlap long reads and then correct/consensus as a separate step (I know this doesn't help getting Canu to do it that way, just following up on colindaven's comment).

Canu corrects reads before overlapping. I don't know if it can be shoe-horned into working on raw reads since it isn't expecting a 15% error rate when it overlaps. Just to offer additional annoyingly non-Canu advice, the flye assembler constructs an assembly graph before read correction.
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