DayTimeMouse

First and foremost, I greatly appreciate your reply. My research goal is to simulate a cancer genome derived from the human reference genome by individually simulating the paternal and maternal...

Yes, I am very interested in your related work and look forward to you posting the link in the future, I will follow it. Finally, I wish you all the...

Hi @yjx1217, Thank you so much, I learned a lot from this paper. Warm Regards.

Hi @yjx1217, I used pbsv(https://github.com/PacificBiosciences/pbsv) to call SVs, then DUPLICATION is called. I want to ask how to set duplication varaints via simuG. Is there any difference between CNV and...

Hi, [zengxiaofei](https://github.com/zengxiaofei) If I use this command: `haphic pipeline allhaps.fa HiC.filtered.bam nchrs --gfa "hap1.p_ctg.gfa,hap2.p_ctg.gfa"` Is HiC.filtered.bam generated by allhap.fa(cat hap1.fa hap2.fa)?Like: `bwa mem -5SP -t 28 allhap.fa read1_fq.gz read2_fq.gz |...

But I do not have real parental genomes, I used hifiasm(HiFi + ONT +HiC) to get hap1.fa and hap2.fa. In this case, do you still recommand me to use Canu(trio-binning...

Many thanks!

Hi， I have another question. How to get haplotype-specific HiC reads(paired-end)? Using haplotype-specific kmers? Best regards.

Many thanks, please let me know if you updated this.

Hi @Arang, But I am still confused about using all HiFi reads to evaluate QV and completeness. Because I want to evaluate each haplotype not primary genome.