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Hi,
How were these three files generated?
- gisaidAndPublic.masked.pb.gz
- results/gisaid/metadata_2022_*_*.tsv.gz
- results/gisaid/epiToPublicAndDate.latest
Thanks!
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KP.1.1.3+A3647G, T7090C, A17585G,G25012T(Orf1a:I1128V,Orf1b:D1373G,S:E1150D)
GISAID query: G25012T,C4999T,A17585G
No. of seqs: 12(Singapore 1 Australia 3 Canada 1 China 1 USA 6)
First: EPI_ISL_…
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(base) d3w@d3w:~/covseq$ python3 preprocess/concatenate_fasta.py -i TRIAL/ -o TRIAL/test.fasta --gisaid_metadata gisaid_hcov19.xls
#########################
# Concatenate all FASTA #
#############…
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**Context**
On Dec 2, 2021, multiple `fetch-and-ingest` runs for GISAID failed. The failure pattern was we would download for a while and the transfer would get closed before it's completed. Subseq…
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![image](https://github.com/user-attachments/assets/9d31be3c-f79a-492a-b659-af384330db36)
tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_60f5_b40c10.json?f_userOrO…
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From branch 110 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253
Like LF.8, this is another lineage messed up by inaccurate proposals of DailyCovidCases.
As it clearly emer…
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I just noticed that ingest is seemingly stuck for at least 2 hours without doing anything? It hasn't yet started any curation. It's not fetching from Genbank nor from GISAID, yet nothing is happening.…
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From branch 115 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253
JN.1+C23039G, T22928C, C21627A(S:T22N, F456L, Q493E)
Or JN.1.16+C23039G,C21627A(S:T22N,Q493E)
Now usher…
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Most seqs on this JN.1.11+S:R346T branch are dropouts from KP.2*. However, there seems to be a real branch hiding inside.
JN.1.11+C7979T, A12463G,T21737C,G22599C, T22928C(S:F59L,R346T,F456L)+G25440…
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Is the training source code available? We want to refer to your [article](https://doi.org/10.3390/ijms232314683) in our paper as a baseline for SARS-CoV-2, comparing our results (not out yet) with you…