I want to extract bacteria from ncbi nt to make a bacteria subset nt database. And use bowtie2 mapping reads with this bacteria subset nt database.
I have find some information at "Vertebrate Subset Nr Database? Build My Own?". I just don't know what I can do now. Many information teach my to use formatdb or blastdbcmd. But it's no use know. NCBI has (or is about to) stopped supporting gi numbers.
Can you give me some information?