How to download all the complete genomes of a bacterium (eg E. coli, Mycobacterium tuberculosis etc) in the .gbk format from NCBI?

Question

[savscosta]

I tried downloading the complete genomes of several bacterial from the NCBI site but i didnt succeed

[Pierre Lindenbaum]

but i didnt succeed

Answer 1

[Joe]

Use Kai Blin's ncbi-genome-download tool. You can pass it a list of the Taxa IDs you want.

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

If you don't know which taxids you need, use the script I wrote which is in the same repository as the tool under the /contrib/ folder

Answer 2

[natasha.sernova]

See my answer in this post:

where can I get environmental bacteria genome in fasta format (as many as possible)?

the .gbk format doesn't exist in NCBI now, you need to transform *.gbff-file to gbk or use another database.

In case you don't need some recent genome versions, search bacterial genomes you need in the file inside the post above.

I've repeated the link below. And these genomes are in gbk-format.

ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/assembly_summary_genbank.txt

Copy the ftp-links you need and download the corresponding genomes, one after another.

how to download all the complete genomes for mycobacteria from NCBI? - this 5heikki's post gives a computational way to do it.