Tag: SARS-CoV-2

Automated Lineage Definitions Now Available in NCBI Virus SARS-CoV-2 Variants Overview

Recently, NCBI Virus SARS-CoV-2 Variants Overview moved from a manual to an automated process for selecting mutations required to define a lineage (e.g., Omicron, BA.2, JN.1, etc.). With this update, the SARS-CoV-2 Variant Overview provides coverage for all SARS-CoV-2 lineages and is no longer limited to only lineages with CDC status. The SARS-CoV-2 Variants Overview website reports results from analyzing both GenBank and unassembled Sequence Read Archive (SRA) sequence data. It allows you to view geographic and frequency trends of records assigned to Pango lineages and search for sequence records using lineage-defining or other mutations (example shown in Figure 1). Continue reading “Automated Lineage Definitions Now Available in NCBI Virus SARS-CoV-2 Variants Overview” →

Successful NCBI-NIAID Codeathon Explored VCF Files in Population Genomics

Variant Call Format (VCF) files provide a crucial way to record and share information about genetic variants across samples. NCBI joined forces with the National Institute of Allergy and Infectious Diseases (NIAID) to co-host the VCF Files for Population Genomics Codeathon (July 31 – August 4). The codeathon focused on innovative methods for harnessing VCF files to analyze large datasets using the COVID-19 Genome Sequence Dataset, sourced from the National Library of Medicine (NLM) and NCBI’s SARS-CoV-2 Variant Calling Pipeline. This virtual event was a booming success and brought together experts in viral evolution, molecular epidemiology, and population genomics.

We received outstanding participation and engagement!

62 participants from academia, government, and industries across the world
8 teams collaborated and worked on the projects listed below
5,000+ views of final presentations
100+ strong applicants
21 different countries represented

Continue reading “Successful NCBI-NIAID Codeathon Explored VCF Files in Population Genomics” →

NCBI Virus: Mutation-Based Search for SARS-CoV-2 Data

Millions of SARS-CoV-2 samples from around the world have been made publicly available as assembled and unassembled sequence data in GenBank and the Sequence Read Archive (SRA). Now you can find sequences with a particular mutation by searching with the protein and the amino acid change (e.g. S:F486V). Visit our SARS-CoV-2 Variant Overview on NCBI Virus and click on the ‘Mutation’ tab to get started (Figure 1).

Figure 1: SARS-CoV-2 Variants Overview. Arrows indicate important features on the page, including the “Lineages” and “Mutations” tabs to switch between views, the search box, and the information box describing the mutation format. The results are also indicated, including a summary of the total records found that contain the searched term as well as the results table. Continue reading “NCBI Virus: Mutation-Based Search for SARS-CoV-2 Data” →

NCBI SARS-CoV-2 Resources Page Will Redirect Soon

End of the COVID-19 Public Health Emergency

During the COVID-19 pandemic, we provided the NCBI SARS-CoV-2 Resources Page as a central location to help you quickly and easily find our SARS-CoV-2 related content and tools. Since the federal public health emergency is now over, this page will be redirected to the SARS-CoV-2 Data Hub in NCBI Virus effective August 1, 2023.

Don’t worry! All this information will remain available. Check out the NLM Knowledge Base to access a list of NCBI SARS-CoV-2 data and tools.

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Questions?

If you have questions or would like to provide feedback, please reach out to us at info@ncbi.nlm.nih.gov.

NCBI-NIAID Beyond Phylogenies Codeathon was a success!

SARS-CoV-2 genomic data is critical for monitoring the viral spread and evolution of the COVID-19 pandemic, identifying newly emerging variants, and developing and evaluating the countermeasures. As of September 2022, over 13 million SARS-CoV-2 genomes have been sequenced across the world, making it the most sequenced pathogen ever. A cornerstone of genomic analysis is building a phylogeny, which demonstrates the relatedness of individual isolates to the rest of the sequenced genomes. However, the volume of SARS-CoV-2 genomes presents novel opportunities beyond phylogenies, as well as computational challenges to traditional methods of genomic analyses and visualization. Continue reading “NCBI-NIAID Beyond Phylogenies Codeathon was a success!” →

Announcing the GenBank and SRA Data Processing Webpage

Interested in understanding how sequence data are submitted, processed, and made publicly available in GenBank and the Sequence Read Archive (SRA)? Announcing the GenBank and SRA Data Processing webpage!

Here you can learn about procedures that the National Center for Biotechnology Information (NCBI), part of the National Library of Medicine (NLM), uses for processing submitted data and public posting, as well as key definitions of data status. Continue reading “Announcing the GenBank and SRA Data Processing Webpage” →

Announcing the NCBI SARS-CoV-2 Variant Calling Pipeline and Related Data Products

Still waiting for an analysis pipeline that can uniformly process raw sequence data produced by a variety of sequencing platforms? Your wait is over! Announcing the SARS-CoV-2 Variant Calling Pipeline, which is now operational and optimized to provide support for multiple sequencing platforms including, Illumina, Oxford Nanopore, and PacBio.

This new pipeline can make allele frequency calls equal to or above 15%. See our publication preprint and our GitHub repository for more details. This optimized pipeline is a result of the efforts of the COVID-19 research community, led by the NIH Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV) initiative, a public-private partnership for a coordinated research strategy to support and speed up the development of COVID-19 treatments and vaccines. Continue reading “Announcing the NCBI SARS-CoV-2 Variant Calling Pipeline and Related Data Products” →

Announcing the NCBI Datasets SARS-CoV-2 taxonomy page

Need SARS-CoV-2 assembled genome sequences or specific SARS-CoV-2 protein sequences? You can find them on the new SARS-CoV-2 taxonomy page brought to you by NCBI Datasets.

The NCBI Datasets SARS-CoV-2 taxonomy page brings you both SARS-CoV-2 genomes and proteins, basic information about SARS-CoV-2, and connections to related NCBI pages, all in one place (see Figures 1 and 2).

Figure 1. NCBI Datasets SARS-CoV-2 taxonomy page. For command-line access, try the datasets command-line tool (top box). For customized filtering options, check out NCBI Virus (bottom box).

If you scroll down the taxonomy page you will find a table of SARS-CoV-2 proteins, each with “Actions” that provide the option to download a package of protein sequences from all annotated SARS-CoV-2 genomes (Figure 2), as well as links to NCBI Gene and the protein sequence from the reference genome.

Figure 2. NCBI Datasets SARS-CoV-2 taxonomy page (cont’d). Click the blue download button to download a package of all SARS-CoV-2 genomes (6 M and counting as of 7/15/22), or just the SARS-CoV-2 reference genome (top box). Below that you see a table of SARS-CoV-2 proteins, each with “Actions” available through the three-dot menu that provides the option to download a package of protein sequences from all annotated SARS-CoV-2 genomes (bottom boxes).

We want to hear from you! Check out the new SARS-CoV-2 taxonomy page and let us know what you think. Contact us with questions or feedback.

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End of the COVID-19 Public Health Emergency

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Questions?

Where and how will I be able to access SARS-CoV-2 normalized data after this change occurs?