Dear altruists, I want to blast against all the bacterial genomes in the command line. But how can I make database for all bacterial genomes? I will be grateful if anyone enlighten me with the necessary informations.
But how can I make database for all bacterial genomes?
That is a rather vague request. Hopefully you have the infrastructure necessary to do this locally since it will take hundreds of GB of disk and RAM. There are literally thousands of bacterial genomes in GenBank.
You could download the genome sequence data using answer here: retrieving entire genomic sequence contents of a database
Once you have the data downloaded it would be usual process of using makeblastdb with this gigantic fasta file of bacterial genomes (that you will need to create).
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