Question: Download All The Bacterial Genomes (previous versions) From NCBI ftp
0
gravatar for Ayish
16 months ago by
Ayish0
Ayish0 wrote:

Hi,

I want to download the all Bacterial genome assembly fasta files from NCBI and I found that there is a master file (ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_refseq.txt) to download the latest version of the whole bacterial genomes. But I am more interested to download the previous version of the genome assembly fasta. Is anyone knows how can I download those or is there any master file on FTP to download the bacterial genomes.

Thanks in advance

assembly • 658 views
ADD COMMENTlink modified 16 months ago • written 16 months ago by Ayish0

Just out of interest, why would you want to download older versions of the assemblies? Do you want to download older versions of the assemblies for a specific bacterial species or all bacterial assemblies available on the NCBI?

ADD REPLYlink written 16 months ago by Sej Modha4.7k

You will find a directory called all_assembly_versions under each bacterial genome folder in GenBank bacterial genomes. Here is one example. There are previous threads about downloading genome assemblies. Using the fie you found and the previous answers you should be able to modify one of them to get the older assemblies.

ADD REPLYlink modified 16 months ago • written 16 months ago by GenoMax92k

Thanks for reply !!.

But I need to download all the bacterial genomes from RefSeq/Genbank and it would be too difficult to look in the directory for every genome for the previously released versions of the genome. Is there any other alternative option to do that ...

ADD REPLYlink modified 16 months ago • written 16 months ago by Ayish0

You won't actually look in each genome folder. You will have to modify the solutions that are available here to fit this rather odd request (since most people generally want/need the latest release).

ADD REPLYlink written 16 months ago by GenoMax92k

Hi, did you find a way to do this? I also want to download all the bacterial genomes of previous version.

ADD REPLYlink written 23 days ago by niuyw30

want to download all the bacterial genomes of previous version

Previous version of what? There may be multiple prior assemblies (like in the example I linked above). You would need to traverse the directory structure to identify those names and decide which one you want (or want them all).

ADD REPLYlink written 23 days ago by GenoMax92k

Sorry I did not make myself clear.

To be specific, I want to download all the bacteria genomes of a previous time, say 2018-08 (about Refseq release 88). Since I downloaded all bacteria genomes at that time, but I accidentally delete them, so, I wanted a version of Refseq of that time point, to reproduce my results. From your answer above, I could get all the previous assemblies, but I could not make sure which ones were the genomes I used before. Thank you for your reply!

ADD REPLYlink written 22 days ago by niuyw30
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