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Usher is an amazing, extremely important tool for my lineage designation workflow. A major time sink/inefficiency right now is that it takes quite long to get an Auspice tree, even if I don't upload a…
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MC.8> C28471T(Orf9b:S63F)
Query: C9803T, A13121T, C28471T
Earliest sequence: 05-20 Sevilla, Andalusia, Spain EPI_ISL_19194903
Latest sequence: 08-04 Stockholm, Sweden EPI_ISL_19333790
Regions de…
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Transferred from sars-cov-2-variants/lineage-proposals#1802
Found with @aviczhl2 's phylogenic tree analysis tool.
Spotted first by @aviczhl2 .
KP.3.1> A1620G(Orf1a:E452G), del29728-29776(#2646…
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# Websites
https://www.shareable.net/blog/how-innovative-funding-models-could-usher-in-a-new-era-of-worker-owned-platform-cooperatives
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I've noticed that when I click the "view in Usher" button, the Usher tree seems to no longer use the public + GISAID tree - using only public sequences. Maybe there's been a change in Usher API?
@A…
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It looks like the new usher-sampled (on dev.usher.bio) can deal with well above 100 sequences 🎉
Unfortunately the usefulness is reduced by not showing details which allows me to quickly open the t…
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When it's time to extend the protobuf format, we should add a list/array of masked sites, so that usher can perform the same masking when the protobuf is initially created and when samples are added t…
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It would really help navigate Usher Auspice trees if `Pango lineage assigned by Usher` was annotated on uploaded samples as well.
I think this shouldn't be too hard given you display this informati…
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### Description
When the nodes have certain special characters a duplicate node is created.
### Steps to Reproduce
1.`usher -t tree.nwk -v aligned.vcf -o tree.pb` Observed in final_tree.nh
2.`…
gp201 updated
8 months ago
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