Join us on June 30, 2021 at 12PM eastern time to learn how to use the new NCBI Datasets resource to find and download gene, genome and SARS-CoV-2 sequence and annotation. You will learn how to access these datasets through either the web interface or the new command-line tools that allow you to incorporate these data in your bioinformatic workflows.
- Date and time: Wed, June 30, 2021 12:00 PM – 12:45 PM EDT
After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI webinars playlist on the NLM YouTube channel. You can learn about future webinars on the Webinars and Courses page.
NCBI Datasets, the new set of services for downloading genome assembly and annotation data (previous Datasets posts), has redesigned and reorganized web pages to make it easier to find and access the services and documentation you need.
NCBI Datasets has a fresh new homepage (Figure 1) highlighting the types of data available through our tools. Available data include genome assemblies, genes, and SARS-CoV-2 genomic and protein data. You can easily access these from the new page or learn more with our new documentation pages.
Figure 1. Features of the new Datasets homepage with quick access to help documentation including the Quickstart and How-to guides as well as access to Genome, Gene, and Coronavirus Data, and the Datasets and Dataformat command-line tools. Continue reading “New NCBI Datasets home and documentation pages provide easier access”
Important Note: Please see our latest documentation on how to download gene ortholog data. The commands below have been deprecated in the latest version of the NCBI Datasets command-line tools.
You can now get gene ortholog data using the NCBI Datasets command-line tool using a gene ID, gene symbol, or RefSeq nucleotide or protein accession. Data are available for vertebrates and insects. The vertebrate orthologs includes a specialized set for fish. (See our recent post for more information on the orthologs for fish and insects.)
You can retrieve metadata for gene orthologs in JSON Format, or you can download a compressed (zip) archive containing both metadata and sequences (Figure 1).
Figure 1. Command-lines that use a gene symbol (BRCA1) to retrieve mammalian ortholog metadata (top, JSON metadata shown in part in the image) and sequences (bottom).
Continue reading “The Datasets command-line tool now provides ortholog data”
In March, we announced NCBI Datasets, a new resource that lets you easily retrieve and download data from across NCBI databases. Did you know you can now fetch NCBI Gene data programmatically using the NCBI Datasets API or command-line tool? Quickly retrieve both metadata and gene sequence data for multiple Gene records including transcripts and proteins in one shell command or API request. The API documentation is a good way to get started with programmatic access (Figure 1).
Figure 1. The Datasets API documentation showing a demonstration retrieving Gene metadata using RefSeq mRNA accessions. The API returns a readily processed JSON object.
Continue reading “Programmatic access to Gene data using Datasets command-line and API”
NCBI Datasets now offers Gene tables: customizable tables of the genes you specify, with key gene information, and the ability to easily download a dataset of genomic, transcript and protein sequences.
Drag and drop a list of Gene IDs or gene symbols, and the data table shows your genes with up to 15 columns of metadata, including genomic coordinates, RefSeq transcript and protein accessions, Ensembl IDs and UniProt accessions, and other gene information. You can browse and select items in your table on the web, or download everything to your computer for later analysis (Figure 1).
Figure 1. The Data tables web download. Top panel. Enter or upload a list of gene identifiers or symbols. Bottom panel. The resulting table display allows you to browse results, download the table or the sequence data for the genes (genomic, transcripts, proteins). Continue reading “NCBI Datasets now provides downloads of gene data for more than 30 thousand organisms”
Do you need to download a lot of data? or maybe you need just a few really big genomes? Prior to the advent of NCBI Datasets, downloading such a large amount of data could be a frustrating and time consuming experience involving failed downloads and writing custom scripts.
Figure 1. Downloading and processing genomic data using NCBI Datasets. The example shows downloading the set of RefSeq primate assemblies through the Datasets web interface. Since the downloaded files would exceed 15GB, the file comes as a “dehydrated bag” — a small, easily downloaded, zipped file with metadata and links to download the data. You can “rehydrate” the unzipped dehydrated files — fill them with the corresponding data — using the datasets command-line tool.
Continue reading “Easily download large amounts of genomic data with NCBI Datasets”
NCBI’s Reference Sequence (RefSeq) FTP release numbers will increment to 200 for the next release and skip over the numbers 100-199. The current, March 2020 release, is release 99. The next bi-monthly release in May 2020 will be release 200. This change is to avoid overlapping with the release numbers of the completely independent RefSeq annotation releases for the eukaryotic genomes we annotate, which are currently in the range 100-109, for example Mus musculus Annotation Release 108. Continue reading “The next RefSeq FTP release number will skip to 200”
We have added the latest NCBI Eukaryotic Genome Annotation Pipeline results for the more than 580 species that we annotate to the genomes/refseq directory on the genomes FTP area. As we announced in December, we will stop publishing annotation results to the genus_species directories (example: genomes/Xenopus_tropicalis) on the genomes FTP site effective February 1, 2020. We will also move existing genus_species directories to genomes/archive/old_refseq during the month of February.Figure 1. The Assembly page for the Xenopus tropicalis UCB Xtro 10.0 (GCF_000004195.4) showing the blue download button. Annotation results such as the RefSeq transcript alignments that can be downloaded from the web page are now also under the genomes/refseq directory on the FTP site. The FTP path to the .bam alignment files is in red.
These FTP changes do not affect the Assembly download function. As always, you can download assembly data using the blue Download button on the web pages (Figure 1).
You can now download new file types for species recently annotated by the NCBI Eukaryotic Genome Annotation Pipeline from the Assembly web pages and from the genomes/refseq FTP area. The new files types include alignments of annotated transcripts to the assembly in BAM format, all models predicted by Gnomon, and — for species that have been annotated multiple times — files characterizing the feature-by-feature differences between the current and the previous annotation.
Continue reading “New download files and FTP directories for genome assemblies”
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 firstname.lastname@example.org. We’d love to hear from you!