Can the software specify the output file name

[Achuan-2]

[kblin]

ncbi-genome-download is designed to handle bulk downloads from the NCBI servers, so being able to specify output file names isn't really part of the feature set. However, if you use the --flat-output and --output-folder parameters when downloading only a single file, it should be straightforward to rename that one downloaded file afterwards. Like this:

ncbi-genome-download --assembly-accessions GCF_008931305.1 --flat-output --output-folder example bacteria
mv example/*.gz example/streptomyces_coelicolor.gbff.gz

Note that this will fail if you download more than one file.