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Merge pull request #1 from nextstrain/fixes
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fixes
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joverlee521 authored Sep 18, 2023
2 parents 34de197 + e85a065 commit c336044
Showing 1 changed file with 2 additions and 2 deletions.
4 changes: 2 additions & 2 deletions ingest/rules/fetch_from_ncbi.smk
Original file line number Diff line number Diff line change
Expand Up @@ -8,13 +8,13 @@ Choose the one that works best for the pathogen data and remove the rules relate
to the other approaches.
1. Fetch from Entrez (https://www.ncbi.nlm.nih.gov/books/NBK25501/)
- Returns all avaiable data via a GenBank file
- Returns all available data via a GenBank file
- Requires a custom script to parse the necessary fields from the GenBank file
2. Fetch with NCBI Datasets (https://www.ncbi.nlm.nih.gov/datasets/)
- Directly returns NDJSON without custom parsing
- Fastest option for large datasets (e.g. SARS-CoV-2)
- Only returns metadata fields that are avaiable through NCBI Datasets
- Only returns metadata fields that are available through NCBI Datasets
- Example is written for viral data, please see offical NCBI Datasets docs for other genomes
"""

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