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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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Polyploidy graph binning of hifiasm #359

Open Iven-gif opened 1 year ago

Iven-gif commented 1 year ago

hi，thanks for your tool !

Author of said they used hifiasm to get the haplotype-resolved assembly of autotetraploid potato. [https://github.com/baozg/Potato_C88]

I want to ask which version of hifisam contain -5 parameter, and what file it need. I don't know the input file format. If it works successfully, what are output files i will get ?

Thank you for your help and wish you all the best.

chhylp123 commented 1 year ago

Please see the scripts here: https://github.com/baozg/Potato_C88. The current release should support -5, although I haven't exposed it in the help information.

zhangyixing3 commented 1 year ago

Does Polyploidy graph binning of hifiasm support aneuploidy? I am very curious about it.

chhylp123 commented 1 year ago

In theory, it should work, but we haven't tried yet.

zhangyixing3 commented 1 year ago

Thanks for your reply. Next I will try Polyploidy graph binning in my species.

Iven-gif commented 1 year ago

Please see the scripts here: https://github.com/baozg/Potato_C88. The current release should support -5, although I haven't exposed it in the help information.

Many thanks. I have tried many times and got the haplotype-resolved assembly in the end. I have one more question: dose polyploidy graph binning could run with HiC and UL data to improve the assembly of primary contigs ?

chhylp123 commented 1 year ago

Please see the scripts here: https://github.com/baozg/Potato_C88. The current release should support -5, although I haven't exposed it in the help information.

Many thanks. I have tried many times and got the haplotype-resolved assembly in the end. I have one more question: dose polyploidy graph binning could run with HiC and UL data to improve the assembly of primary contigs ?

We could have a try to see if it could work, but it may take time.