Tag: GDH

New in NCBI Datasets: Species pages and species browser

NCBI Datasets introduces species pages and species browser! The species pages summarize taxon information and provide access to genomic data, including reference genomes. For example, see Figure 1, the Nothobranchius furzeri (turquoise killifish) species page.

Figure 1: Nothobranchius furzeri species page. The browse species button will take you to the species browser. 

Continue reading “New in NCBI Datasets: Species pages and species browser”

Sept 22 Webinar: Using NCBI Datasets command-line tools to access data and metadata for genomes

Sept 22 Webinar: Using NCBI Datasets command-line tools to access data and metadata for genomes

Join us on September 22, 2021 at 12PM eastern time learn to use the datasets command-line tools (datasets and dataformat) to access, filter, download, and format data and metadata for genomes. Through examples from eukaryotes and the SARS-CoV-2 coronavirus, you will see how to use metadata to filter for genome sequences with desired properties such as genomes with high contig N50 values.

  • Date and time: Wed, September 22, 2021 12:00 PM – 12:45 PM EDT
  • Register

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.

Vertebrate Genome Project genome assemblies annotated by NCBI

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 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”