Tag: Datasets

Vertebrate Genome Project genome assemblies annotated by NCBI

NCBI is an active partner of the Vertebrate Genomes Project (VGP), who recently published a series of papers on the initial results of their efforts to sequence all 70,000 vertebrate species. See the VGP press release for more details. To date, this project has submitted over 130 diploid chromosome-level assemblies to NCBI’s GenBank and the European Nucleotide Archive. NCBI has annotated 94 of the VGP assemblies from 85 species using the NCBI Eukaryotic Genome Annotation Pipeline.

These sequence and annotation data are available through NCBI web resources including Gene, Assembly, Nucleotide, Protein, and Datasets and are included in the GenBank and RefSeq releases. You can browse the assemblies in the Genome Data Viewer and download metadata, sequence, and annotation data for the latest assemblies in the VGP BioProject using the NCBI Datasets command-line tools as shown below. Continue reading “Vertebrate Genome Project genome assemblies annotated by NCBI” →

NCBI at CSHL Biology of Genomes, May 11 – 14, 2021

NCBI staff will be presenting virtual posters at the Cold Spring Harbor Laboratory Biology of Genomes Meeting, May 11 -14, 2021. The posters will cover the following topics: 1) a cloud-ready suite of tools (PGAP, RAPT , and SKESA) for assembling and annotating prokaryotic genomes, 2) Datasets — a new set of services for downloading genome assemblies and annotations, and 3) updates on NCBI RefSeq eukaryotic genome annotation, and the Genome Data Viewer (GDV). Read more below for the full abstracts.

The virtual poster gallery opens Tuesday, May 11 at 9:00 a.m. with dedicated time for poster viewing and discussion at 1:00 to 2:00 p.m. through Slack each day. The poster gallery will be open for entire the conference and remain available for six weeks afterwards. Continue reading “NCBI at CSHL Biology of Genomes, May 11 – 14, 2021” →

Data for SARS-CoV-2 variants now available at NCBI

Looking for genomes for the B.1.1.7 SARS-CoV-2 variant? NCBI now supports searches for SARS-CoV-2 variant names such as B.1.1.7, B.1.351, or P.1. For example, search for B.1.1.7 (Figure 1) and you’ll see a virus classification box with an option to download a SARS-CoV-2 data package. SARS-CoV-2 data packages include genome and protein sequences and a detailed data report for all SARS-CoV-2 genomes classified as that variant. SARS-CoV-2 genome lineages are classified by pangolin, using the pangoLEARN algorithm.

Figure 1. SARS-CoV-2 variant search result with button to download a data package containing data for all SARS-CoV-2 genomes matching that variant lineage, B.1.1.7 in this case.

Continue reading “Data for SARS-CoV-2 variants now available at NCBI” →

New NCBI Datasets home and documentation pages provide easier access

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” →

The Datasets command-line tool now provides ortholog data

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” →

Announcing the RefSeq annotation of rat mRatBN7.2!

NCBI RefSeq has finished its initial annotation of the new rat reference assembly, mRatBN7.2, recently released by the Darwin Tree of Life Project at the Wellcome Sanger Institute. This is the first coordinate-changing update to the rat reference since the 2014 release of Rnor_6.0 from the Rat Genome Sequencing Consortium and brings the rat assembly into the modern age with a nearly 300x increase in contig N50 and 9x increase in scaffold N50 lengths. It’s a major improvement!

Continue reading “Announcing the RefSeq annotation of rat mRatBN7.2!” →

NCBI on YouTube: RAPT and BLAST+ on the Cloud, SARS-CoV-2 genome data in Datasets

It’s time we do another roundup of what’s been happening on YouTube!

First up, the NCBI YouTube channel has merged with the NLM YouTube channel. You’ll now be able to find diverse content all on one channel, from tips on using resources to fascinating moments in the history of medicine and more!

Continue reading “NCBI on YouTube: RAPT and BLAST+ on the Cloud, SARS-CoV-2 genome data in Datasets” →

Retrieve genome data by BioProject using the Datasets command-line tool

You can now retrieve genome data using the NCBI Datasets command-line tool and API by simply providing a BioProject accession. You can go directly from a BioProject accession to genome data even when the BioProject accession is the parent of multiple BioProjects (Figure 1).

Figure 1. Command-lines using BioProject accessions with the datasets command-line tool and sample metadata. Top panel: command-line for downloading genome metadata for the Sanger 25 Genomes Project (PRJEB33226). Middle panel: a portion of the metadata in JSON format for the 25 Genomes Project. Bottom panel: command-line for downloading sequence data and annotation metadata for a component BioProject for the king scallop (PRJEB35331). Continue reading “Retrieve genome data by BioProject using the Datasets command-line tool” →

Programmatic access to Gene data using Datasets command-line and API

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 Presents Two Online CoLabs at ASHG 2020!

Two up-and-coming NCBI resources will be featured in videos, surveys and live events at the American Society for Human Genetics (ASHG) 2020 Annual Meeting. Come and watch on-demand videos in the CoLab Theater. Then, let us know what you think and how you do or might use these resources by either taking an online survey or joining us for the CoLab Live! Events on Thursday, October 29, 2020.

Continue reading “NCBI Presents Two Online CoLabs at ASHG 2020!” →