If you download data from the SRA (Sequence Read Archive) FTP site, we would encourage you to try the SRA Toolkit. This is particularly true if you use the SRA Fuse/FTP site at ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant, which the SRA team will decommission on December 1, 2019.
The SRA Toolkit offers several advantages for downloading SRA data, including greater flexibility in specifying the data you need as well as access to public SRA data in the cloud. If you’re new to the Toolkit, you may want to start with these instructions.
If you have any questions or concerns about downloading SRA data, please contact email@example.com. We’d love to hear from you!
On Wednesday, November 15, 2017, at 12:00 PM EST, NCBI will present a webinar on advanced applications of the NCBI APIs we previously introduced in our general API webinar in September. This webinar is intended for bioinformaticians, computational biologists and others who are already comfortable with writing scripts to access, download and analyze data.
This blog post is directed toward PubMed users.
Did you know you can download the entire PubMed database, and keep this dataset current with our daily update files? These data are available for free from our FTP site and no longer require a license agreement, whether you’re interested in text mining, or want to create your own database for searching and analytics.
Each year in December, NLM releases a comprehensive (baseline) set of citation records in XML format for download. Every day, incremental update files are made available and include new, revised and deleted citations. Please see the README.txt file for more information and contact firstname.lastname@example.org with questions.
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.