HapHiC
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HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data
pore-C data
Hello, @zengxiaofei Can HapHiC input porec data? If not, what adjustments do I need to make? Thank you in advance for your response
Hello, Xiaofei. I'm having some small issues with HapHiC. My species is an autotetraploid (2n=4x=44), and I used p_utg generated by hifiasm as the input file. When clustering, the command...
Hi , I used haphic for allotetraploid genome (2n=4x=44). It makes 22 groups like the following which have huge variations in chromosome sizes as given below and can be seen...
Hello @zengxiaofei , I used hifiasm with hifi and HiC data, and generate haplotype-specific data, including p_ctg.fa, p_utg.fa, r_utg.fa, and hap*.p_ctg.fa. As you mentioned in the tutorial, if I want...
Hi, I am trying to use HapHiC to anchor a haplotype-collapsed genome (hifiasm p_ctg), and I found that HapHiC perform not so good, **especially contig ordering,** HiC data was mapping...
Hi there Is it possible to implement support for BED files along with BAM and PAIR formats? Best regards
Thank you for your excellent work! I wonder if I run the haphic pipeline correctly. I have a genome of 4G (a diploid, 2n=26), and I just use the p_ctg.fa...