I have about 75x coverage of 10X Genomics Chromium data for a non-model reptile species. I've used this to produce a genome assembly using Supernova and am currently using similar coverage of Hi-C data to scaffold. I expect this scaffolding process to result in assembly gaps of various lengths beyond what is already probably present in my Supernova assembly.
I know there is lots of software for filling gaps using short Illumina reads and dedicated software for long-read data like PacBio, but I wondered if there is any software that leverages the linked Illumina reads provided by 10X Genomics to perform gap-filling? Or is there a way to extract the assemblies of linked reads from Supernova (or produce de novo) that should theoretically provide contig sequences up to the length of the input molecules, which could be used with a custom mapping pipeline to fill gaps?