How to get BLAST wgs database

Question

[Michael]

I would like to "mimic" the online BLASTn wgs search (NOT nt, this works already) on my local machine. The reason is that I want to extend from the BLAST nt search to a broader range of bacterial strains.

It seems like there is no BLAST wgs database to download. How do I determine which genomes I have to download to catch the genomes in wgs. I only need it for bacteria for a start.

An alternative would be to not use the entire wgs but some method to at least "broaden" the search compared to BLAST nt.

Answer 1

[GenoMax]

Did you take a look at this README file NCBI provides for instructions on how to deal with WGS data with blast+? Scripts you need are in this directory. Bacteria are taxid 2.

[Michael]

That's really cool! This means that the data is first downloaded to the local machine to execute the search, right? So the search is not performed on NCBI servers?

[GenoMax]

You should check that by using a specific bacterial taxid first (e.g. Pseudomonas etc). If the data is downloaded locally then you had better have access to plenty of local storage :-)

[orenmn]

(credit to https://github.com/khyox/draftGenomes/issues/1)

IIUC, taxid2wgs doesn't report all wgs records. for example:

perl taxid2wgs.pl 90371 | grep AAJDPJ

would return nothing, even though https://www.ncbi.nlm.nih.gov/assembly/GCA_007903735.1 exists.