Download genomes from assembly file

[ChillarAnand]

Feature Request:

There is new database FDA-ARGOS. For this we can download assembly file from https://www.ncbi.nlm.nih.gov/bioproject/231221

How to download all the genomes from the assembly file?

[kblin]

I don't think it's ncbi-genome-download's job to understand those files.
Having said that, it should be trivial to write a little script to convert this file into one that ncbi-genome-download understands.

Something like this should work:

grep -e "^#" -v  /PRJNA231221_AssemblyDetails.txt | cut -d$'\t' -f1 > accs_to_download.txt
ncbi-genome-download --section genbank --assembly-accessions accs_to_download.txt --progress-bar bacteria