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Hi, @maximilianh
It's a useful tool for submitting viral sequences in bulk.
I am wondering to know if it was possible to provide submission of pathogenic sequences other than COVID-19 (e.g influe…
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It seems that S:F456L is very convergent in JN.1 now. (**last complete update June 19**)
- [*] Branch 1: JN.1.1.2+S:F456L, #1147 DEAD
- [*] Branch 2: JN.1.1+C9142T+S:F456L, #1249 DEAD
- [x] Bran…
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- [x] GISAID using their CLI API
- [x] NCBI - BioSample
- [x] NCBI - Genbank
- [x] NCBI - SRA
- [x] NCBI - Table2asn
cc: @leebrian @rchau88 @kristinelacek
nbx0 updated
10 months ago
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Need to automate the upload of files to these different sources
GISAID
- Need to fix header errors
Github
Google Cloud
- No need to wait for analysis to be complete to start this. In a fully au…
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**Brief description**
* Error encountered in `gisaid_uploader` `parse_fasta`
* Additionally, error did not appear to propagate to Slack or cron email
**Pipeline exit code:** [Exit code]
***
…
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Hi Max,
Regarding the upload token for GISAID. In the manual for the CLI uploader there is a test token.
Cheers,
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Yesterday's GISAID upload was interrupted by a brief outage. The pipeline had reached the step where it was communicating updates to the GISAID API with `gisaid_uploader`. I manually raised the outbou…
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Please note this comment: [https://github.com/nextstrain/ncov/issues/53#issuecomment-612454452](url)
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* [x] `institute.ena_assembly_opted`
* [x] How to get process information in scope (`process.bioinformatics.pipeline.pipe`) for `ocarina-get-ena-assembly.py`
* [x] How to get `ENA-SAMPLE` and `ENA-R…