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schatzlab / genomescope

Fast genome analysis from unassembled short reads
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Higher heterozygosity #109

Open shehongbing opened 1 year ago

shehongbing commented 1 year ago

hi, there, I performed genome survey using HiFi reads. And my command as follows:

kmc -k27 -m24 -cs10000 pigweed.HiFi.fq.gz pigweed ./ kmc_tools transform pigweed histogram pigweed.histo -cx10000

The results as follows: http://qb.cshl.edu/genomescope/genomescope2.0/analysis.php?code=ffiaSWwLPRS0FLXEUp1D

I was puzzled about the high heterozygosity (7.34%), but almost one peak is found. Would you mind give me some suggestions.

thx hongbing

mschatz commented 1 year ago

I agree it is not a great fit. I think it is getting confused by the relatively high rate of error. Have you used DeepConsensus on the reads? That often cleans up the data nicely

Good luck! Mike

On Tue, Sep 5, 2023 at 2:03 AM shehongbing @.***> wrote:

hi, there, I performed genome survey using HiFi reads. And my command as follows:

kmc -k27 -m24 -cs10000 pigweed.HiFi.fq.gz pigweed ./ kmc_tools transform pigweed histogram pigweed.histo -cx10000

The results as follows:

http://qb.cshl.edu/genomescope/genomescope2.0/analysis.php?code=ffiaSWwLPRS0FLXEUp1D

I was puzzled about the high heterozygosity (7.34%), but almost one peak is found. Would you mind give me some suggestions.

thx hongbing

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