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Confused about the assembly results with Hi-C data.
Dear writer,
I was very confused about the assembly results with Hi-C data.
I used hifiasm to assemble a triploid genome, and the result looks perfect with N50 > 15M and contig-quantity about 760. Some contigs even approach to chromosome.
But when I use them to scaffold by juicer, the Hi-C heatmap is extremely sparse. Even 2/3 of the length of a 35M contig has none Hi-C signal. What caused this?
One more question, a region of a haplotype always missing no matter how I modify the parameters, how to supplement?
Appreciate and look forward to your reply!