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Thank you for this tool!
I have successfully run the GCE and is able to get gce.log and gce.table
PFA
[gce.log](https://github.com/fanagislab/GCE/files/12333292/gce.log)
but now I am confused a…
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Hi @ochoudhu
I did not find any proper answer on Heterozygosity awareness in the paper ! Does your tools take care of heterozygosity? How does it deal with heterozygous region?
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Something like
```
def individual_heterozygosity(ts, ind):
ts.pairwise_diversity(ind.nodes)
```
should do it - very simple, but we want to make it easy and natural for people to deal with indi…
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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…
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Hi, thanks for scikit-allel.
It looks like the current implementation of `heterozygosity_observed` is suitable for diploids but not polyploids.
The current implementation treats all heterozygous…
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Hi I'm trying to run nPhase on a tetraploid yeast genome I seqeunced with PacBio HiFi reads.
Here is my code:
`nphase pipeline --sampleName trialRun1 --reference s288c.fa --longReads pacbioHiFi…
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Hi,
I have been using pbsim3 to simulate HiFi read data and reassemble it to get acquainted with long read assembly. An issue I encountered is the relative cleanness of the simulated data. I used t…
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Hi,
First of all, thank you very much for developing these nice scripts. I just have a stupid question regarding the heterozygosity rate. How can I calculate it? Thank you very much.
Best wishes…
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Can you briefly describe how KAT calculates the heterozygosity rate reported in the json file?
For one of my genome assemblies, the heterozygosity rate =0, but I believe that is an artifact of the hi…
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Hello, I used Jellyfish to assemble the histogram plot that I plugged into the GenomeScope2 interface. This work is being done on a diploid crayfish genome. I need help interpreting the very slanted n…