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.
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?
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 :-)
(credit to https://github.com/khyox/draftGenomes/issues/1)
IIUC, taxid2wgs doesn't report all wgs records. for example:
would return nothing, even though https://www.ncbi.nlm.nih.gov/assembly/GCA_007903735.1 exists.