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Flagged [internally](https://support.nextstrain.org/agent/nextstrain/nextstrain/tickets/details/668036000007764001) by @rneher that the acknowledgements download does not include the GISAID isolate ID…
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Dear colleagues,
I was wondering if you could share the details on how you did the bulk download of .fasta sequence data from GISAID / EpiCov?
That would be very helpful.
Many thanks,
best,
Sophi…
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For users who want to use GISAID data with this workflow, the following steps work _nearly_ as expected.
These steps assume you have downloaded:
- all sequences in FASTA format with whitespace …
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## Context
Our automated workflows use short lived AWS credentials for sessions which are limited by the [max_session_duration](https://github.com/nextstrain/infra/blob/814a7e4cd635b40c12fb0c4e83b168…
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5 assemblies from GISAID QC'd through HIVE3.
Raja's idea: Hit submit -> pop-up saying "Do you want you download the metadata from GISAID?"
Jonathon has to do some research on f programmatic access …
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From branch 33 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1502
KP.2.5+C592T+C2377T, del21653_21655(Orf1a:N704K,S:S31del)
GISAID query: T592C,T2377G,A22115G
No. of seqs: …
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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 https://github.com/sars-cov-2-variants/lineage-proposals/issues/1666
GISAID reads this mutation as T21994C+del21998_22000, resulting in S:H146del instead of the S:Y144del for normal JN.1*s.
H…
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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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- Revisar esquema Gisaid (Maria Lara)
- relecov-tools map para gisaid
- relecov-tools upload-to-gisaid usando multisub https://github.com/maximilianh/multiSub