Incorrect assembly size

[cblazier]

stderr.verkkoZZZZZZZMALE.txt

I have two strains of a 3.4 Gb mammalian genome, for which I have good coverage of PacBio and UL ONT generated in house using identical methods. The first strain assembles well to a genome of the expected size, a size consistent with other assemblers' results and with flow cytometry. The second strain assembles into something almost 6 Gb in size, inconsistent with other assemblers and flow cytometry.
I have attached the stderr file for the "bad" genome assembly. Please let me know what additional information I might provide to help figure out why one assembly is bad and the other good.
Thanks,
CB

[skoren]

I don't see any kind of phasing information (trio/hi-c) input in the logs. Verkko will not output pseudo-haplotypes so I suspect one of your genomes is more homozygous and comes out close to the expected size because of that while the second one is being split into two haplotypes and so is much larger.

[cblazier]

Interesting, thanks. That's indeed possible, though they are both lab strains that we expect to be rather inbred (and appear to have low heterozygosity in the k-mer histograms). I will try again using Hi-C data and report back.