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zengxiaofei / HapHiC

HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data
https://www.nature.com/articles/s41477-024-01755-3
BSD 3-Clause "New" or "Revised" License
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Number of chromosmes if using two pseudo haplotypes from hifiasm #1

Closed chregu1971 closed 11 months ago

chregu1971 commented 1 year ago

Hi, If I combine hap1 and hap2 from hifiasm for scaffolding. Do I have to set the number of chromosomes to the haploid or diploid number? Best regards, Christian

zengxiaofei commented 1 year ago

Hi, If I combine hap1 and hap2 from hifiasm for scaffolding. Do I have to set the number of chromosomes to the haploid or diploid number? Best regards, Christian

Hi Christian,

You should set the number of chromosomes nchrs to the diploid number.

If you are uncertain about the exact number of chromosomes, you can also try the quick view mode.

It is worth noting that scaffolding multiple haplotypes with extremely low heterozygosity, such as human genomes, remains a challenge for all existing scaffolders. This is because that most of the Hi-C reads mapping to these haplotypes will be filtered out with a loose threshold of MAPQ >= 1. In these cases, you may still need to scaffold each haplotype separately.

Best wishes, Xiaofei