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.
Did you take a look at [this README][1] file NCBI provides for instructions on how to deal with WGS data with `blast+`? Scripts you need are in [this directory][2]. Bacteria are `taxid 2`.


  [1]: ftp://ftp.ncbi.nih.gov/blast/WGS_TOOLS/README_BLASTWGS.txt
  [2]: ftp://ftp.ncbi.nih.gov/blast/WGS_TOOLS/