Tag: GenBank
The current release has:
Sequence data from the ongoing avian influenza A (H5N1) virus outbreak in cattle are now available through NLM’s NCBI resources NCBI Virus and NCBI Datasets.
These data were submitted by the U.S. Department of Agriculture (USDA), U.S. Centers for Disease Control and Prevention (CDC), the World Health Organization (WHO), Iowa State University, and St. Jude Children’s Research Hospital. Continue reading “New Data Available! Access Avian Influenza A (H5N1) Virus Sequences at NCBI”
The National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM) and other Founding Members of the International Nucleotide Database Collaboration (INSDC) have enhanced its website, www.insdc.org, to provide comprehensive information on how interested parties from around the world can evaluate their readiness to participate in the INSDC. This effort supports INSDC’s aim to broaden membership and attract qualified nucleotide sequence databases. Web content now includes a formalized Founders Arrangement and a Membership Arrangement, along with other updated information about the INSDC mission, vision, governance, and technical documentation. In doing so, INSDC encourages interested parties to visit the INSDC website to learn more. Continue reading “International Nucleotide Database Collaboration (INSDC) Introduces Enhanced Website”
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”
GenBank release 260.0 (4/19/2024) is now available on the NCBI FTP site. This release has 31.18 trillion bases and 4.46 billion records.
The current release has:
Do you submit genome assembly data to GenBank? If so, try out NCBI’s Foreign Contamination Screen (FCS) tool, a quality assurance process that you can run yourself. We will screen all prokaryotic and eukaryotic genome submissions to GenBank with this tool, but we encourage you to screen your data before submitting to save time. FCS offers sensitive contaminant detection to increase the quality of your genome submissions to GenBank. As part of our ongoing effort to improve your experience, we recently made several enhancements. Continue reading “Foreign Contamination Screen Tool: Now Available in Galaxy!”
GenBank release 259.0 (12/22/2023) is now available on the NCBI FTP site. This release has 27.94 trillion bases and 3.96 billion records.
The current release has:
As announced earlier this year, we will begin to systematically gather ‘location of collection’ and ‘date and time of collection’ for sequence data submitted to GenBank and the Sequence Read Archive (SRA).
As part of this effort and to make location data more accurate and informative, we are also changing the way this information is represented on GenBank records, consistent with the relevant field in BioSample. Continue reading “Update to GenBank Qualifier”
GenBank release 258.0 (11/2/2023) is now available on the NCBI FTP site. This release has 26.74 trillion bases and 3.85 billion records.
The current release has:
Coming soon! As part of our ongoing effort to enhance your experience and modernize our services, several of our legacy virus-related web resources will be replaced by NCBI Virus – our community portal for viral sequence data. NCBI Virus is more comprehensive, modernized, and has more powerful features and analysis tools than our legacy resources.
Below is a list of the legacy virus resources that will be replaced by NCBI Virus. The list includes a description of features that will continue to be supported through NCBI Virus: Continue reading “Upcoming Changes to Virus Data Resources at NCBI”