High percentage of ambiguous bases.

[keith-harrison]

Hi I am trying to assemble genomes of other strains using another strains reference and am getting good matches from what I can see using mauve. I first created contigs using flye and medaka. However, I am now having the issue of a high N % in my assembly. Apologies if I have just missed a tool parameter!

ntJoin assemble target=polished.fasta references=reference.fasta t=12 target_weight=1 reference_weights=2 n=2 w=250 k=32 19% Ns When I used homopolish after medaka this gave me 28% Ns.