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**Context**
A common use case for the ncov workflow is for users to download GISAID data for a specific analysis (e.g., a state-focused build) and combine other existing metadata they have about thos…
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Hello, we are the Stanford HIVDB team and we are building an open source [SARS-CoV-2 in vivo selection research database](https://covdb.stanford.edu/search-drdb/selection-data/). The database so far c…
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Another case of intra-host prolonged infection like Sabin22. SRA/GISAID sequences are both available. Discuss this with Bob first before entering.
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Previously only in Japan, now spreads to other countries.
KP.3.3+G23856T(S:R765L)
GISAID query: G23856T, C28291A, G28884C
No. of seqs: 25( Japan 23 South Korea 1 Ireland 1)
First: EPI_ISL_1914…
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LB.1.2.2 >C22075T (S:V171V silent ) >C23029T (S:Y489Y silent ) > S:S704L (C23673T), M:L29F (C26607T)
Query: C23673T, C26607T,C23029T
Samples: 9 ( plus one from Nevada not on Gisaid yet9
Countries:…
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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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It was raised to my attention that the collection dates of certain strains from the GISAID database are mislabeled. For example, EPI_ISL_480757 was labeled as 2020-12-06. To refrain from making our ow…
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Hi, there:
I am trying to follow the Github instructions to test CovdGenotyper.
I am wondering wherther I should create a "data" folder in the same level as CovidGenotyper or within it.
The…
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Add a table of SRA/Genbank/GISAID/VIC IDs to enable easier sorting of what is in each database, and allow users to query the databases for sequences of interest.
This is in response to issue #2.