I have asked a similar question before, but I am in a similar but different situation.
I have assembled the genome of a wild animal species (XY species) in Hifiasm.
The coverage is about 34x, and I don't know which is the Y chromosome and which is the X chromosome
because the genome of a closely related species is not read.
The coverage is supposed to be halved for the sex chromosomes, so I do not know how the output will look.
I have three questions for the output files of Hifiasm.
I assembled with the default settings, and among the outputs, the resulting gfa files are:
hifiasm_*.bp.r_utg.gfa
hifiasm_*.bp.p_utg.gfa
hifiasm_*.bp.p_ctg.gfa
hifiasm_*.bp.hap1.p_ctg.gfa
hifiasm_*.bp.hap2.p_ctg.gfa
First, is it possible that
hifiasm_*.bp.hap1.p_ctg.gfa
hifiasm_*.bp.hap2.p_ctg.gfa
harbor X-linked and Y-linked sequences, respectively?
In my case, since "hifiasm_.bp.hap1.pctg.gfa" and "hifiasm.bp.hap2.p_ctg.gfa" have different sizes, I think it is possible.
My second question is if it is ok for us to assume that hifiasm_.bp.pctg.gfa is the logical sum of hifiasm.bp.hap1.pctg.gfa and hifiasm*.bp.hap2.p_ctg.gfa?
Finally, is it correct to assume that hifiasm_.bp.putg.gfa contains sequences (potential sex chromosome sequences) that are not included in hifiasm.bp.pctg.gfa, hifiasm.bp.hap1.pctg.gfa and hifiasm.bp.hap2.p_ctg.gfa?
Hello.
I have asked a similar question before, but I am in a similar but different situation.
I have assembled the genome of a wild animal species (XY species) in Hifiasm. The coverage is about 34x, and I don't know which is the Y chromosome and which is the X chromosome because the genome of a closely related species is not read.
The coverage is supposed to be halved for the sex chromosomes, so I do not know how the output will look. I have three questions for the output files of Hifiasm.
I assembled with the default settings, and among the outputs, the resulting gfa files are:
First, is it possible that
harbor X-linked and Y-linked sequences, respectively? In my case, since "hifiasm_.bp.hap1.pctg.gfa" and "hifiasm.bp.hap2.p_ctg.gfa" have different sizes, I think it is possible.
My second question is if it is ok for us to assume that hifiasm_.bp.pctg.gfa is the logical sum of hifiasm.bp.hap1.pctg.gfa and hifiasm*.bp.hap2.p_ctg.gfa?
Finally, is it correct to assume that hifiasm_.bp.putg.gfa contains sequences (potential sex chromosome sequences) that are not included in hifiasm.bp.pctg.gfa, hifiasm.bp.hap1.pctg.gfa and hifiasm.bp.hap2.p_ctg.gfa?
Best, Jung