Hap1 is smaller in size and has a low contig N50, while Hap2 is larger and has a higher contig N50.

[afiyachida]

Hello,

I am currently trying to assemble a shrimp genome (Genome size: 694 Mb). Hifiasm ran smoothly without errors, however, the principal haplotype had very low contig N50 of 36,128 bp. Whereas the alternate haplotype has ~2Mb. Is there a reason why this could be happening ? What would be the best way to sort this ?

hifiasm \ -l 1 \ --n-hap 2 \ --hg-size 694380k \ -o data_169.asm \ -t 64 \ data_169.trim.fastq.gz

Thank you, Afiya