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duo haplotyping about hifiasm HOT 4 CLOSED

chklopp avatar chklopp commented on May 31, 2024
duo haplotyping

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Comments (4)

lh3 avatar lh3 commented on May 31, 2024

An interesting use case. In theory, there should be an algorithm that can generate phased assembly with just one parent (to lower accuracy in comparison to trio binning). However, hifiasm doesn't support this use case yet and implementing it will take time. We will keep this in mind. Thanks.

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shilpagarg avatar shilpagarg commented on May 31, 2024

Yes, adding to Heng's comment: I think WHdenovo algorithm (https://github.com/shilpagarg/WHdenovo) in principle can generate phased assemblies for any variants of pedigrees. We have designed this tool for Illumina and long-read data types. From our experiments, we observe that this method works fine for genome sizes up to 500 Mb and repeats 10-20%. I am happy to work with you to help you solve your use case. Let me know.

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chklopp avatar chklopp commented on May 31, 2024

The genome we are assembling has 2% heterozygocity. The kmer count histogram show a nice bimodal distribution. To produce the yak paternal file for hifiasm we would need to perform three operations on the HiFi and maternal yak files. One would be to chunk the HiFi kmer file to separate the homozygous and heterozygous kmer using minimum and maximum coverage thresholds (kind of yak split), the second, to find heterozygous kmers which a not in the maternal file (kind of yak diff) and the last to join homozygous and partenal heterozygous kmer (kind of yak merge).

Yak code (https://github.com/lh3/yak) does not seem to have these functions.

Another solution would be to perform this with another tool, for example kmc, and then to format the resulting file in yak format.
Is there a script to format a kmer count file in yak format?

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chhylp123 avatar chhylp123 commented on May 31, 2024

I guess the second solution might be better. If you want to do it manually, I recommend you to partition corrected reads by yourself, and then feed the partitioned lists to hifiasm by the option '-3' and '-4'.

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