I'm using canu, and I want to know if it's possible to just use MHAP to find alignment and use PBDAGCON or falcon_sense just to generate consensus sequences, then not to assembly the consensus sequences. I see MHAP has many parameter settings, but I see only a few in the canu documentation. I have a few questions: 1. If I want to use all the parameters in MHAP, is that possible via canu? 2. If I just need to use MHAP and PBDAGCON for consensus, is canu a good choice? If not, should I use PBcR-MHAP instead or something else? 3, Are the consensus from MHAP and PBDAGCON like some short contigs assembling from original long reads(Are the consensus must be bigger than the original long reads)?
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