Comments (4)
In the GFA files, the 'HG:A' column of A-line indicates which haplotype does this read come from.
'HG:A:m': from maternal haplotype
'HG:A:p': from paternal haplotype
'HG:A:a': not binnable
HiCanu has its own trio-binning mode + read partition mode, it should be better to directly use HiCanu since there might be some bias. I guess the read partition steps of both HiCanu and hifiasm are comparable. The major difference is how to generate the final contigs. BTW, if you want to evaluate the phasing results, I'd like to suggest you to evaluate by yak and merqury, instead of only merqury. HiCanu shares the same partition parts with merqury. So it may have bias.
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yes, I also used yak triobin
and found contigs which belongs to one haplotype genome was marked as "a", "m" and "0" , but also "p" was found in this genome. Since I provided parental NGS data to yak
then run hifiasm
, why this genome still contain another haplotype reads which used to assemble.
here is my yak trio
resultes:
h1tg000111l p 63 0 64 2 0 0 27001 423
h1tg000112l p 10552 0 13600 0 16 1 101022 169
h1tg000113l p 2035 0 2057 2 4 7 39954 864
h1tg000114l a 17 0 18 10 3 0 25055 256
h1tg000115l p 121 0 183 0 0 0 37708 93
h1tg000116l p 122 0 208 34 19 26 49258 1694
h1tg000117l p 307 0 459 0 4 1 59201 89
h1tg000118l m 0 19 1 23 4 0 353381 23
h1tg000119l p 410 0 545 4 0 0 46710 98
h1tg000120l p 11214 0 14826 8 5 1 114096 137
h1tg000121l p 105 0 176 0 0 0 38161 70
Another question is reads used to for assembling two haplotypes are 213719 and 220259. 72583 were not binnable. But my total hifi ccs reads were 3703697.
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Just make sure: are you only passing paternal index to hifiasm for assembling, and then evaluate by yak trioeval with both paternal and maternal indexes?
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sorry, I used the wrong command. But I have evaluated phasing completeness using merqury. Both Hifiasm and Canu-trio got good results. I also used yak trioeval
but cannot understand the results well even read this issuse. Thanks for your help!
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Related Issues (20)
- Output interpretation with HiFi+ONT+HiC with inbred samples + `-l0` HOT 1
- low BUSCO scores HOT 1
- Mitigate Overlapping Sequence Assignments in Haplotypes HOT 3
- Help!!! Segmentation fault (core dumped) HOT 1
- Question about the depth of ONT ultra-long reads HOT 1
- Homotetraploid, super-large genome, with different parameters, the size of p_utg varies greatly? HOT 1
- setting K parameter in yak HOT 2
- how to make the correct genome size estimation for allotetraploid species? HOT 2
- Possible missing one haplotype in human assemblies HOT 2
- No haploid.gfa files output in trio-binning mode HOT 3
- Hifi + Hi-c + ONT assembly fails
- In Trio-binning, always more on hap1 despite (almost) same sequences for paternal and maternal
- discontinuous assembly with shorter pacbio hifi reads but high coverage HOT 2
- Is x20 of Hifi data enough to construct draft assembly of 6.5Gb genome? HOT 1
- line 8: 110334 Aborted(core dumped) HOT 1
- Ultra Long intergration failed: no output for UL kmer counting HOT 3
- missing 8Mb sequences in the assembly HOT 5
- Empty haplotype 2 gfa files by ONT integration HOT 1
- Basic Question About HiFi Input HOT 3
- Spend too long times to run hifiasm HOT 1
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