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KP.3.1.1+C5826T(Orf1a:T1854I)+C8247T, G22104T(Orf1a:S2661F, S:G181V)
GISAID query: C5826T, C8247T, G22104T
No. of seqs: 16(France 1 Germany 2 Luxembourg 2 Spain 1 Sweden 1 USA 8(2 from Portugal))
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Hello, I'm trying to run a next strain analysis using gisaid data. (export augur needed data from gisaid). After exporting the data (fasta and metadata files). I made my own configuration file (attach…
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Hi,
Thank you so much for this excellent tool. I've been using it as an efficient way to query many sequences from across a region.
Lately I've been having some trouble downloading sequences and m…
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XEC>> C19983T > T1993C, Orf1a:M1771V (A5576G = PLPro_M208V) , Orf1b:P1664S (C18457T) [Edited]
tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1787b_845120.json?f_…
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Transferred from sars-cov-2-variants/lineage-proposals#1971
JN.1.67.1> G1126A> T21738C(S:F59S), G22599C(S:R346T)
Query: T21738C, G22599C, G26660T
Query for dropout sequences: G4162A, T21738C, G22…
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Transferred from sars-cov-2-variants/lineage-proposals#2026
KP.3.1.1> C1441T> A26760C(M:I80L), G28423C(Orf9b:R47P)
Query: A26760C, G28423C
Earliest sequence: 07-22 New York City, New York, USA …
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Dear,
We are using your tool on spiked samples and come across some discrepancies between what we expect and what we get. For example we used a bought RNA virus at 100% that should be B.1.1.7 (this…
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We have a single case where public dataset (`data://garden/covid/latest/combined` and hence our full covid dataset) depends on private dataset `data-private://garden/covid/latest/sequence`.
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data…
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It is probably worth collecting instances where we think that we have got recombinations wrong for various reasons. Here's one, which involves recombination within the XB lineage, between a grandchild…
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I can run the code and it will open up GISAID and put in my login details. However, it cannot hit the login button or proceed any further.