This blog post is directed toward Assembly users.
A new “Download assemblies” button is now available in the Assembly database. This makes it easy to download data for multiple genomes without having to write scripts.
For example, you can run a search in Assembly and use check boxes (see left side of screenshot below) to refine the set of genome assemblies of interest. Then, just open the “Download assemblies” menu, choose the source database (GenBank or RefSeq), choose the file type, and start the download. An archive file will be saved to your computer that can be expanded into a folder containing your selected genome data files.
Specific instructions for downloading genomic FASTA sequence for all RefSeq bacterial complete genome assemblies are provided in the Genomes Download FAQ. Simple variations on these steps can be used to obtain different file types or data for different sets of genome assemblies.
This is a beta-test version of this new functionality, and we welcome your feedback!