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When analyzing genomes with varying recombination rates, the length threshold for identifying identical by descent (IBD) segments cannot be constant when measured in base pairs (bp). To obtain accurat…
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**Description**
**Sub-lineage of:** JN.1.16.1
**Earliest sequence:** 2024-6-24, Senegal
**Most recent sequence:** 2024-7-27, Australia, Western Australia — EPI_ISL_19333883
**Continents circulatin…
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**Description**
I was able to run the main pipeline, I used bakta as an annotator instead of prokka
I am not able to run neither summary command or the pangenome workflow using panaroo. I think it…
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Often users need to create their own custom models.
It would be good to show the process of inheriting from a FESTIM class to override some methods etc
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It'd be nice if the summary table listed the number of children below each node of:
- donor 1
- donor 2
- recombinant
I tried to find this in the table but couldn't.
In particular, I'd love t…
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Metadata about particles is useful and currently includes things such as a cached log likelihood, but could also include a cached ML distance estimate or other information. Currently metadata is store…
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In https://github.com/jeromekelleher/sc2ts/issues/130#issuecomment-1470438214 the `sample_subgraph(712029)` plot shows 3 inserted (i.e. non-sample) nodes which appear to be completely redundant: 67365…
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**Description**
**Sub-lineage of:** JN.1.39 (JN.1 + G2782T)
**Earliest sequence:** 2023-11-27 – USA, Ohio — EPI_ISL_18609351; England — EPI_ISL_18598897
**Most recent sequence:** 2024-3-25 – China,…
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Dear whom it may concern,
I hope everything is well with you.
I am running tsinfer+tsdate for a vcf file generated from SLiM. It works well for a small sized vcf file but returns an assertion er…
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I am going to make a synthetic bolometer diagnostic for WEST tokamak, based on SOLEDGE3X-HDG and ERO2 codes.
The plasma will contain deuterium as main ions and tungsten as impurities.
I was going …