I want to assemble my study genome use PacBio long sequence and Bionano with Hybrid-Scaffold way.
Firstly, I assemble the contigs use PacBio long sequence and the resulted have only 0.1% N.
Then, I assemble the scaffolds use Bionano data (Direct Label and Stain (DLS) chemistry ) as the suggestion in Bionano Solve Theory of Operation: Hybrid Scaffold. But the assembly results have too much N (nearly 27%) and the genome size is increased compared to the k-mer assess.
So, whether I ignore some parameters and what should I do for getting the best assembly results?
Any help is much appreciated. Thanks.