Access GISAID with NEXTSTRAIN

[abombin]

Hello, our group recently started to use Nextrain for the processing of SARS-2 data and it works great, that far!
The one step that limits the efficiency of the whole workflow is the necessity to download the data from GISAID, accessing it through a browser. Does Nextstrain include any tools that can allow to include data acquisition step (from GISAID) in the pipeline?
Thank you,
Andrei

[james]

Hi Andrei - unfortunately we are not able to provide direct access to GISAID data. We can make available all of the GenBank (open) data in nextstrain formats - see here for more.

[corneliusroemer]

Hi Andrei, sorry for the late response. I think this answer could be helpful for you:

GISAID download augur input

Hi @omarkr, I’m sorry for the late reply. Nextstrain is completely separate from GISAID, so my answer should only be seen as suggestions from a fellow GISAID user (not authoritative). As far as I’m aware, none of the GISAID users I know can download more than 5000 entries via the web interface. This seems to be a restriction placed by GISAID. I don’t know why, you would have to ask GISAID. However, some researchers have been given “API” access by GISAID, which is basically a special, private,…