Output interpretation with HiFi+ONT+HiC with inbred samples + -l0

[AndreaGuarracino]

How should I interpret hifiasm outputs when I have HiFi+ONT+HiC of an inbred sample as input, and I use -l0?

With HiFi and HiFi+ONT, -l0 gives a healthy primary assembly, and a shorter and fragmented alternate assembly. This is expected, having a homozygous inbred sample.

With HiFi+ONT+HiC, -l0 gives a primary assembly that is a bit worse than the primary assembly made with HiFi+ONT, no alternate assembly, and two haplotype-resolved assemblies (*.hic.hap[1|2].p_ctg.*). One of these haplotype-resolved assemblies looks better than the primary assemblies made with HiFi+ONT and HiFi+ONT+HiC, the other is shorter and worse than those.

[baozg]

If you use HiC for phasing, the -l0 shouldn't work anymore (not purge dups or phasing). It should be similar to -l3 with purge haplotypes. In my experience, the HiC phasing for inbreeding samples would generate two similar haplotypes except for the long heterozygous regions. For the contiguity, another explanation may be hifiasm try to put all unresolved short contigs into haplotype1 #623