missing 8Mb sequences in the assembly about hifiasm HOT 6 OPEN

Hi @xzhoubayer, sorry for the late reply. Could you please double check if these missing contigs could be found with a_ct.gfa?

from hifiasm.

Hi @xzhoubayer, sorry for the late reply. Could you please double check if these missing contigs could be found with a_ct.gfa?

I don't see the a_ct.gfa file. This is the list of gfa file I have:
asm.bp.hap1.p_ctg.gfa
asm.bp.hap1.p_ctg.noseq.gfa
asm.bp.hap2.p_ctg.gfa
asm.bp.hap2.p_ctg.noseq.gfa
asm.bp.p_ctg.gfa
asm.bp.p_ctg.noseq.gfa
asm.bp.p_utg.gfa
asm.bp.p_utg.noseq.gfa
asm.bp.r_utg.gfa
asm.bp.r_utg.noseq.gfa

from hifiasm.

Is your sample homozygous? If it is, it would be better to run hifiasm with -l0, which will be able to disable purge_dups. To get a_ctg. please add --primary as well.

from hifiasm.

it is relatively homozygous. I triled -l 0, no difference.
I will try --primary and update you.

from hifiasm.

I tried --primary and -l0, no improvement. The mapped read still do not show up in asm.bp.p_ctg.gfa and asm.bp.a_ctg.gfa.

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I also encountered a similar problems. I have a 2Mb missing sequences in the tail of hap2. Some methods were conducted to check and I tend to it would be a missing assembly.

1. I checked the normal 2Mb sequences in hap1, it contains the telemore sequence. Thus, it is reasonable that this sequence is at the end of the chromosome.
2. The HiC heatmap shown that this 2Mb is corrected located there.
3. Syntenic mapping by syri indicated that the 2Mb is indeed completely missing, not a large segment missing in the middle of the chromoseome.
4. I also extrated this 2Mb contig from hap1, and mapping it to hap2 (as a ref in minimap2) by minimap2 asm5, no highly similar fragments were found, only very short local alignments.

The first pic is hap1 which contain the 2Mb seqeucne.

This second pic is hap2 which miss the 2Mb sequence.

The third is a syntenic mapping by syri, which was conducted by minimap2 asm5

Sincerely appreciate anyone who can give me some advice, I have tried to modify many parameters, such as improve -D -N --n-weight --n-perturb --f-perturb -s -u.

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