We work with a VERY complex genome. It is a pathogen, with a large genome size at around ~240Mb. By complex, I mean, we have done PacBio sequencing and FALCON assembly, yet only got about 0.6 Mb N50 values.
In order to try to consolidate our genome into manageable segments (e.g. pseudochromsomes) we decided to utilize both BioNano optical maps and DoveTail HiC. Both methods relied on high molecular weight DNA.
Alas, neither method significantly improved our assembly in terms of N50, even though both assembled the FALCON pacbio contigs in different ways. DoveTail increased N50 from about 0.60Mb to 1.15Mb and a relaxed version of the BioNano pipeline increased the N50 to 916kb. The default parameters were, of course, lower.
MY QUESTION IS...are there any commonly used programs that can consolidate hi-C/opticalMap/pacBio assemblies? Many of the examples I see rely solely on Illumina assemblies, but those typically include mate pair libraries, which nonetheless don't contain the same kind of data as our Illumina PE datasets + optical maps + Hi-C maps. I have looked around and found "Metassembler" and "GAM-NGS", as well as "runBNG" and "BionaniAnalyst", but our group isn't very experienced in this kind of de novo assembly with a VERY difficult genome.
Any Advice would be appreciated.