search

chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
535 stars 87 forks source link

triploid assembly and usage of HiC #195

Open YuChrming opened 3 years ago

YuChrming commented 3 years ago

Dear Author I am assembling a triploid material genome which is about 1GB by HiFi and HiC data,use hifiasm 0.16.1-r375. My result of command shown as follow: command : hifiasm --primary -t 42 --n-hap 3 -o sample.asm --h1 good_1.fq.gz --h2 good_2.fq.gz ccs.fastq.gz results : a.ctg.fa = 1.994G hap1.p_ctg.fa = 1.173G hap2.p_ctg.fa = 842M p_ctg.fa = 834M

command : hifiasm --primary -t 42 --n-hap 3 -o sample.asm ccs.fastq.gz results : a_ctg.fa = 1.21G p_ctg.fa = 822M

And I have 3 questions: 1.Considering HiC data may be used in AllHic next , if I could use it in hifiasm? Could I use it twice? 2.The size is considerable difference from expected, which could I employ? 3.For triploid assembling and genotyping, does hifiasm apply to? If you have some strategy or suggestion for me ? Thanks a lot!

chhylp123 commented 3 years ago

Current hifiasm Hi-C phasing method only supports diploid samples. We have some preliminary results on polyploid samples but releasing it still takes time. I'm not familiar with AllHiC so probably you should open an issue on their repo.