I have two fly genomes from a species for which there are no other genomes available. One genome has been assembled from PacBio reads (N50=~400,000bp) and one from 10X (N50=~250,000bp). The genome is about 250-300Gb long.
I would like to use the scaffolds from both these genomes to create an assembly with longer scaffolds.
I have tried
metassembler (https://sourceforge.net/projects/metassembler/) but it requires mate pairs to find the correspondences between the assemblies and I do not have such paired-end reads.
What tools would you recommend to produce longer scaffolds from multiple assemblies?
Here is a list of software I am presently considering: