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There seems to be a test that is only run in CI but missing from the dev documentation.
It'd be great if the person who added the line to the CI config `- run: bash tests/builds/runner.sh` could ex…
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### Solution to issue cannot be found in the documentation.
- [X] I checked the documentation.
### Issue
I used the ARM mambaforge to install mamba on my apple silicon M1.
My base environm…
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Currently auspice can run “locally” such that datasets are sourced from the user’s computer. This is fantastic, but requires an internet connection to load a number of cross-origin resources (see belo…
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### Transferred from https://github.com/sars-cov-2-variants/lineage-proposals/issues/1573
**Description**
**Sub-lineage of:** KP.3.1 (JN.1.11.1.3 = JN.1 + S:F456L, Q493E, V1104L)
**Earliest sequenc…
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## Context
As part of [a separate issue related to IQ-TREE and this workflow](https://github.com/iqtree/iqtree2/issues/40), we learned that the minimum branch length for IQ-TREE with SARS-CoV-2 data …
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KP.3.1+C21812A, C29416A(S:L84I)
GISAID query: C21812A, C29416A, G15372T
No. of seqs: 17(Canada 1 UK 5 Ireland 2 USA 9(2 from Austria, 2 from Turkey))
First: EPI_ISL_19162555, USA from Austria, …
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From branch 41 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253
JN.1+S:L176F+S:F456L, Query: C22088T,C18894T,T22928C,-17562
No. of seqs: 33 (Australia 1 Canada 2 China 6 Fran…
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From branch 25 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253
JN.1.3+S:F456L
Query: T3565C,T22928C,C27945T,-C4777T
No. of seqs: 96
[usher](https://nextstrain.org/fetch/ge…
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**Context**
I've been running builds locally to get context surrounding 21K viruses and I'd like to again flag `augur filter` subsampling as a major performance bottleneck. Here, I'm starting fro…
trvrb updated
1 month ago
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From branch 62 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253
JN.1+G17562T+S:F456L
Query: G17562T,T3565C, T22928C,-8716
No. of seqs: 62 (Australia 1 Canada 13 China 1 Denm…