The new and developing NCBI Datasets resource
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NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Search with an organism (NCBI Taxonomy) and download genomic sequences, annotation and/or metadata datasets.
If you want a quick download of data (example: Measles morbillivirus, Listeria monocytogenes or Candida auris reference genomes) or get a very large dataset (example: all the almost 6,000,000 "Severe acute respiratory syndrome coronavirus 2" genomes) - use NCBI Datasets!
| NOTE: This is a new and still developing resource! It is under continuous development and the team is looking for feedback on what it does well, what could work better, what helpful things could be added..... Let us know! |
You can do this!
Get genome metadata for all assemblies for an organism and its subspecies using the organism name.
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- Start the NCBI Datasets homepage (https://www.ncbi.nlm.nih.gov/datasets/) and in the "Find a species" box, begin typing in the name of your organism and pick an autocomplete suggestion - to help you!
This may take you to a new NCBI Datasets taxonomy page, where you will be able to find some information about and be able to download the Reference (or Representative) genome.
OR
If there are multiple assemblies available for your organism, you'll go directly to an NCBI Datasets Genome page with a filterable, customizable metadata table - and be able to download this genome assembly metadata information or the sequences themselves as a "Package" of data!
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- Alternatively, NCBI Datasets also provides different ways as well as the instructions to access and download this data with a Command-line Tool or using Python or R
For more advanced work:
- NCBI Datasets How-To Guides
- Download NCBI Datasets' command-line tool
- Help with NCBI Datasets APIs and Python or R libraries
- NCBI videos on YouTube:
- NCBI Minute Webinar: "Using NCBI Datasets for Downloading Sequence and Annotation for Genomes and Genes" (June 30, 2021)
- NCBI Minute Webinar: "Using NCBI Datasets Command-line Tools to Access Data and Metadata for Genomes" (September 22, 2021)
- Quick Tutorial: "Easy Access to NCBI Data with NLM's NCBI Datasets!" (July 20, 2022)
Last Reviewed: August 5, 2022