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I need to retrieve COVID-19 metadata (such as date of collection of sequence data, location, etc.) for a batch of 3953 GISAID accessions from the GISAID database.

I am not very comfortable with GISAID. I would prefer an NCBI database solution.

Any help would be appreciated.

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2 Answers 2

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You can download the full db and and put out anything you want with your favourite scripting language.

To do so, you need to request an account first. Once you log in, scroll down to the bottom of the download options. There are 2 meta-data download options, pick what you need.

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  • $\begingroup$ You need to request an account first. Once you can login scroll down to the bottom of the download options and there's 2 meta data download options, pick what U need. $\endgroup$
    – Liam McIntyre
    Jul 11, 2021 at 5:01
  • $\begingroup$ Well done, hope U won't mind I added it to your answer. $\endgroup$
    – Kamil S Jaron
    Jul 11, 2021 at 12:16
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The NCBI link to the metadata database is here

If I get a moment I'll talk you through it.

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