The World Health Organization (WHO)declared the recent upsurge of the mpox virus to be a public health emergency of international concern. Having timely viral genome data freely and widely available enables researchers to explore how this virus differs from viruses isolated and sequenced in the past. Therefore, NCBI’s GenBank is expediting the release of mpox data by annotating gene and coding region features as part of the submission process.Continue reading “Quick & Easy Access to Mpox Data Through NCBI Virus”→
Sequence Read Archive (SRA)dataavailable via the Google Cloud Platform (GCP)are migrating from multi-region to single region us-east-1.This migration is projected to be complete by May 2024. To minimize the impact of this change, we recommend updating your workflow to access SRA data in us-east-1 region as soon as conveniently possible.
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”→
NCBI is excited to introduce Pebblescout, a pilot web service that allows you to search for sequence matches in very large nucleotide databases, such as runs in the NIH Sequence Read Archive (SRA) and assemblies for whole genome shotgun sequencing projects in Genbank – faster and more efficiently!
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 mutationby searching with the protein and the amino acid change (e.g.S:F486V). Visit our SARS-CoV-2 Variant OverviewonNCBI 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”→
Beginning April 2023, we will move the SARS-CoV-2 normalized data and source files from the COVID-19 data buckets on Amazon Web Services (AWS) and Google Cloud Platform (GCP) to the NIH NCBI SRA on AWS registry. We will also remove the SARS-CoV-2 original format data from AWS and GCP COVID-19 buckets and make them available in AWS cold storage. If you need these data, you can request them using the Cloud Data Delivery Service (CDDS).
Where and how will I be able to access SARS-CoV-2 normalized data after this change occurs?
Do you submit or access Sequence Read Archive (SRA) data? In an ongoing effort to enhance your experience, NCBI is making several improvements to our widely used SRA database. SRA is the largest publicly available repository of high throughput sequencing data. The archive accepts data from all organisms as well as metagenomic and environmental surveys. SRA stores raw sequencing data and alignment information to enable reproducibility and facilitate new discoveries through data analysis.
What improvements is NCBI making?
More transparent: We recently launched the GenBank and SRA Data processing page to help you better understand how sequence data are submitted, processed, and made publicly available.
More efficient: Faster data transfers, downloads, and analyses! We will be incrementally streamlining how you access SRA data as SRA Lite becomes the standard SRA file format. This simplified format reduces the average file size for more efficient analysis and storage of large datasets.
More reliable: A trusted source! SRA is a trustworthy database, and we are continuously improving our processes to ensure system reliability.
