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,

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.

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