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The genome download service in the Assembly resource makes it easy to download data for multiple genomes without having to write scripts. To use the download service, run a search in Assembly, use facets to refine the set of genome assemblies of interest, open the "Download Assemblies" menu, choose the source database (GenBank or RefSeq), choose the file type, then click the Download button to start the download. An archive file will be saved to your computer that can be expanded into a folder containing the genome data files from your selections.
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The genome download service is best for small to moderately sized data sets. Selecting very large numbers of genome assemblies may result in a download that takes a very long time (depending on the speed of your internet connection). Scripting using rsync is the recommended protocol to use for downloading very large data sets (see below).
We recommend using the rsync file transfer program from a Unix command line to download large data files because it is much more efficient than older protocols. The next best options for downloading multiple files are to use the HTTPS protocol, or the even older FTP protocol, using a command line tool such as wget or curl. Web browsers are very convenient options for downloading single files even though they will use the FTP protocol because of how our URLs are constructed. Other FTP clients are also widely available but do not all correctly handle the symbolic links used widely on the genomes FTP site (see below).
Replace the "ftp:" at the beginning of the FTP path with "rsync:". E.g. If the FTP path is _001696305.1_UCN72.1, then the directory and its contents could be downloaded using the following rsync command:
Replace the "ftp:" at the beginning of the FTP path with "https:". Also append a '/' to the path if it is a directory. E.g. If the FTP path is _001696305.1_UCN72.1, then the directory and its contents could be downloaded using the following wget command:
NCBI redesigned the genomes FTP site to expand the content and facilitate data access through an organized predictable directory hierarchy with consistent file names and formats. The site now provides greater support for downloading assembled genome sequences and/or corresponding annotation data with more uniformity across species. The current FTP site structure provides a single entry point to access content representing either GenBank or RefSeq data.
Files for old versions of assemblies will not usually be updated, consequently, most users will want to download data only for the latest version of each assembly. For more information, see "How can I download only the current version of each assembly?".
For some assemblies, both GenBank and RefSeq content may be available. RefSeq genomes are a copy of the submitted GenBank assembly. In some cases the assemblies are not completely identical as RefSeq has chosen to add a non-nuclear organelle unit to the assembly or to drop very small contigs or reported contaminants. Equivalent RefSeq and GenBank assemblies, whether or not they are identical, an