How to download all Pseudomonas aeruginosa Genomes from NCBI Genomes database?

Question

[Optimist]

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

Answer 1

[shenwei356]

https://github.com/kblin/ncbi-genome-download
https://github.com/pirovc/genome_updater

Answer 2

[vkkodali_ncbi]

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

[GenoMax]

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

[EricC_NCBI]

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/