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## TODOs
- [x] verify GISAID metadata output
- [x] verify open metadata output
## Context
Determined as the root cause for https://github.com/nextstrain/forecasts-ncov/issues/104
Both the…
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When I upload a fasta file with some 240 sequences to Usher through the file picker, I get the following (error?) screen instead of the normal results:
I definitely didn't upload anything that's …
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XDV.1+C23277T(S:T572I)
GISAID query: C23277T, C11572T, T22930A
No. of seqs: 4( Singapore 2 Canada 2)
First: EPI_ISL_19160979, Canada, 2024-5-5
Latest: EPI_ISL_19181069, Singapore, 2024-5-25
…
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Formerly known as FLIRT Branch 63 (spotted by @aviczhl2)
Defining:
JN.1.11.1 > Orf1b:A2143V (C19895T) > S:R346T (G22599C)
Query : C19895T,G22599C,T3565C
Samples: 5 On Gisaid from Australia , …
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This proposed lineage was first found by @aviczhl2 in [this issue.](https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253)
GISAID Query: T17556C, G22781A
First Seq: EPI_ISL_18963344…
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**Describe the bug**
This may be a bug in the JSON produced by the UShER web interface, not Galago, but they're not working together yet so let's figure it out.
**Expected behavior / How to repr…
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Currently, GISAID ingest takes ~4 hours. We should profile the pipeline to figure out if improvements can be made without a major overhaul (i.e. incremental ingest with caches or a database).
- On…
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Despite number of seqs is not too many, this lineage is present in uploads of multiple undersampled regions.
JN.1.18+C22311A(S:T250N)
GISAID query:C22311A,G22599C,C28958A
No. of seqs: 7(USA 1 …
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Jotting down the outline of ingesting the metadata and sequences from https://github.com/andersen-lab/avian-influenza
1. Fetch tarball of https://github.com/andersen-lab/avian-influenza
2. Concate…
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**Description**
**Sub-lineage of:** KP.3
**Earliest sequence:** 2024-5-5, Canada, British Columbia — EPI_ISL_19161088
**Most recent sequence:** 2024-5-11, Canada, BC — EPI_ISL_19169116, EPI_ISL_191…