How to download all Pseudomonas aeruginosa Genomes from NCBI Genomes database?
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2.1 years ago
Optimist ▴ 180

Hello All,

I want to download all the Genomes of Pseudomonas aeruginosa from NCBI genomes database. As of now (23/10/2020), there are 5556 genomes for species Pseudomonas aeruginosa.

Kindly let me know a way to download all of them. Preferably with strain name .

Thanking You

NCBI Genome Assembly database download • 1.2k views
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2.1 years ago
vkkodali_ncbi ★ 3.4k

You can download these data directly from NCBI using the Datasets tool. Check out: NCBI Datasets for more details.

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Note: Web interface for NCBI datasets only provides access to Eukaryotic genomes. Use command line option for all genomes including bacteria.

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NCBI Datasets now provides access to data for viruses and prokaryotes, including Pseudomonas aeruginosa.

While our Genomes page is limited to a maximum of 1,000 genomes for a single download, you can use the datasets command-line tool to download 15,365 Pseudomonas aeruginosa genomes.

Since this is such a large dataset, at about 30 GB compressed for genome sequence and metadata, I recommend you try this simple three-step approach:

  1. Download a dehydrated data package for all Pseudomonas aeruginosa genomes, including genome sequence and metadata. This only includes metadata.

    datasets download genome taxon "pseudomonas aeruginosa" --exclude-genomic-cds --exclude-protein --exclude-gff3 --filename aeruginosa.zip --dehydrated

  2. Extract the downloaded package.

    unzip aeruginosa.zip -d aeruginosa

  3. Rehydrate the extracted package to get the genomic sequences.

    datasets rehydrate --directory aeruginosa/

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