many fragment sequence in the p_ctg

[chhylp123]

many fragment sequence in the p_ctg

[chhylp123]

Did you run hifiasm on a dataset with very high coverage? Sometimes high coverage may introduce weird things.

[kevfengler227]

many of the small contigs in plant genome assemblies represent variants of telomeric/knob repeats. I typically set the min contig length to 60kb. Even with that, after hybrid scaffolding with BioNano, almost all of the unscaffolded leftovers will be telomeric/knob repeats.

[libenping]

@chhylp123 @kevfengler227 Thank you for the reply! Yeah, the coverage is about 77X, and I will try to assemble with lower coverage (maybe 30-40x) ,Thank you .