I have downloaded viral genomes from the NCBI website I want to use formatdb so I can create a BLAST database of these viral genomes. However, they are present as nearly 300 folders, each containing the fasta files for each of the genomes/genome segments (named by NC_ ids). In the documentation for formatdb, it says to format multiple files I must quote the input files to be formatted. I do not have a list of these files as they are within the folders. Is there any way to formatdb using multiple folders/directories rather than the individual fasta files?
Any help much appreciated :-) Thanks