doc: ncbi datasets

[j23414]

Description of proposed changes

Since the transition from NCBI Virus to NCBI datasets, revised the documentation to reflect changes in how metadata and sequences are fetched from NCBI.

Feel free to propose alternative wording or descriptions.

Related issue(s)

• 82ace30
• Copy ingest dengue#13 (review)

Checklist

• Checks pass

[joverlee521]

Thanks for updating the docs here! (I should have done this as part of #179.)

I recommend adding a "Software requirements" section (similar to the phylogenetic/README) that points to the centralized Nextstrain installation docs instead of adding detailed docs on the NCBI Datasets here.

NCBI Datasets CLI is included in the docker/conda runtimes and would not need to be installed separately. Once we add ncbi-datasets-cli to our ambient installation instructions, the centralized installation docs should cover everything. Then we wouldn't need to maintain separate docs within each pathogen repo that uses NCBI Datasets.

[j23414]

Thanks @joverlee521! Updated centralized Nextstrain installation docs in nextstrain/docs.nextstrain.org#172 and added a software requirments section. This PR is ready for review.