Downloading bacterial reference genome

Question

[Harry]

Hi, I have some bacterial species that I would like to download reference genomes for. I am using the NCBI-genome-download tool. However, it downloads multiple files for one species, can anyone please help why it would do that? I have limited experience in this field...

Answer 1

[shenwei356]

use genome_updater

Top assemblies:

The top assemblies (-j) will be selected based on the species/taxid entries in the assembly_summary.txt and not for the taxids provided with -g "taxids:...". They are selected sorted by categories in the following order of importance: