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In case anyone is interested in the credibility of the national-level daily confirmed cases, see the Appendix of [ArXiv:2007.11779](https://arXiv.org/abs/2007.11779) = [zenodo.4432080](https://zenodo.…
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The page title is "Coronavirus COVID-19 (2019-nCoV)". Since the virus was [renamed](https://www.sciencemag.org/news/2020/02/bit-chaotic-christening-new-coronavirus-and-its-disease-name-create-confusio…
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Since SARS-CoV (which caused the [2002–2004 SARS outbreak](https://en.wikipedia.org/wiki/2002%E2%80%932004_SARS_outbreak)) is better studied than SARS-CoV-2 a lot of knowledge can be mapped from there…
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When running Artic on a sample with too few reads, resulting in too small coverage, Longshot automatically calculates the maximum coverage as 0, and fails. We're having issues with that in an automati…
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From https://github.com/sars-cov-2-variants/lineage-proposals/issues/1509
Other than KP.1.1.1(S:K182N), other seqs on the Orf1b:L2213F branch of KP.1.1 have another NTD mutation set that usher does…
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![image](https://github.com/sars-cov-2-variants/lineage-proposals/assets/78371872/542f10c0-1b0f-4a8f-9934-29fbf5ff9171)
![image](https://github.com/sars-cov-2-variants/lineage-proposals/assets/783718…
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Dear Andrew:
Can I use snp-sites to process the full FASTA data that I downloaded from GISAID, which has about 1,000,000,000 lines in total for ~2 million SARS-COV-2 genomes?
I run it on my lo…
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We have examples where there is a choice of two primers for the end of a given amplicon. Only one primer of the two primers has support from the reads.
Observed behaviour: Both primers are kept, in…
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**Describe the bug**
> 2024-05-30T07:02:00.279-04:00 127.0.0.1 - - [30/May/2024:11:02:00 +0000] "GET /metadata/sourceControlList HTTP/1.0" 200 201 "-" "ELB-HealthChecker/2.0" 0
2024-05-30T07:02:00.3…