hifiasm output: 731.928 MB single contig

[B10inform]

hifiasm output: 731.928 MB single contig

[chhylp123]

Could you please run hifiasm with '-l0' and see what the result looks like? Thanks in advance.

[lh3]

Which tool are you using? Are you sure the tool itself is correct? How did you convert GFA to FASTA?

[B10inform]

Hi chhylp123,

This is my output with -I0 :
Main genome scaffold total: 928
Main genome contig total: 928
Main genome scaffold sequence total: 714.223 MB
Main genome contig sequence total: 714.223 MB 0.000% gap
Main genome scaffold N/L50: 11/23.151 MB
Main genome contig N/L50: 11/23.151 MB
Main genome scaffold N/L90: 45/1.178 MB
Main genome contig N/L90: 45/1.178 MB
Max scaffold length: 52.188 MB
Max contig length: 52.188 MB
Number of scaffolds > 50 KB: 342
% main genome in scaffolds > 50 KB: 97.19%

The genome size is bigger than i am expecting. My genome size is ~400MB. What would be the good way to work with this? Heterozygosity is ~3.5

Thank, happy holidays.

[chhylp123]

Which tool are you using? Are you sure the tool itself is correct? How did you convert GFA to FASTA?

Thanks. As Heng said, which tool did you use to covert GFA to FASTA and calculate N50?

[B10inform]

awk '/^S/{print ">"$2;print $3}' PB4.asm.p_ctg.gfa > PB.asm.p_ctg.fa

[chhylp123]

Interesting. Is it possible that you can share the bin files with us? If not, could you please try Purge_dups on -l0 assembly?

[conchoecia]

Assembly problems aside, I suggest making a Hi-C heatmap against the contig to see if the assembly makes sense, or if it has concatenated several chromosomes together.