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.