Virus web interface, whole-database nucleotide FASTAs (RefSeq and Genbank) can be downloaded as a single nucleotide text file with a single click.
There are 9507 RefSeq viral entries as complete genomes. In terms of nucleotides, that is at least 2-3 orders of magnitude less than a corresponding compendium for bacteria. Frankly, I would be surprised if the file you are referring to contains all RefSeq viral genomes, but I am definitely not surprised that a single file does not exist for all bacterial RefSeq genomes.
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Mensur Dlakic
To my knowledge, there isn't an equivalent direct programmatic way to do this. It is possible to download all the fast files as text files directly though (see for instance
ncbi-genome-download). I would be surprised ifcat-ing the files takes that long though, so you should be able to concatenate them all.If you cant even concatenate a file of that size, you're going to struggle to do any meaningful downstream analysis with something that unwieldy too, so you may need to reconsider your approach.
Thanks Joe. By ncbi-genome-download, do you mean a third party shell script / an Entrez query / a web portal?
Yes, I would certainly give cat -ing a go - if I absolutely had to.
Once I've got the single text file, even if it is hundreds of GB in size, I've found it's perfectly possible to run practical analysis on it with packages like HMMER.
ncbi-genome-downloadfrom Kai Blin is a utility program that will download genomes for you. You can also use NCBI's newest program calledDatasets. More here.This doesn't address the question. These utilities download data to separate compressed archives. I am specifically looking for a single flat file download for multiple genomes - as is currently available in the NCBI virus portal - but for prokaryotes.
There is no pre-created file for prokaryotic genomes. You will need to make it yourself by downloading the genomes.
You could try to create a fasta file from
ref_prok_rep_genomes, which is a pre-formatted blast database NCBI makes available on their blast db FTP site. You can useblastdbcmdtool with the data files. This fasta would contain representative genomes as the name says. Perhaps that may work for whatever you are trying to do.Thank you, but as I mentioned in my question I am looking for the entire prokaryote RefSeq and Genbank databases.
There is no such file. You will have to do it the same way everyone else does it and download the genomes separately. You can parse the ftp addresses from the assembly summary files. All RefSeq bacteria is 600-700GB and all GenBank bacteria +1TB. Generally you would want files which fit on the RAM of your computer. That being said, you can zcat the archives, no?