Sold by: National Library of Medicine (NLM)
Open data
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Deployed on AWS
This repository within the [ACTIV TRACE initiative](https://www.nih.gov/research-training/medical-research-initiatives/activ/tracking-resistance-coronavirus-evolution-trace) houses a comprehensive collection of datasets related to SARS-CoV-2. The processing of SARS-CoV-2 Sequence Read Archive (SRA) files has been optimized to identify genetic variations in viral samples. This information is then presented in the Variant Call Format (VCF). Each VCF file corresponds to the SRA parent-run's accession ID. Additionally, the data is available in the parquet format, making it easier to search and filter using the Amazon Athena Service. The SARS-CoV-2 Variant Calling Pipeline is designed to handle new data every six hours, with updates to the AWS ODP bucket occurring daily.
Overview
This repository within the ACTIV TRACE initiative houses a comprehensive collection of datasets related to SARS-CoV-2. The processing of SARS-CoV-2 Sequence Read Archive (SRA) files has been optimized to identify genetic variations in viral samples. This information is then presented in the Variant Call Format (VCF). Each VCF file corresponds to the SRA parent-run's accession ID. Additionally, the data is available in the parquet format, making it easier to search and filter using the Amazon Athena Service. The SARS-CoV-2 Variant Calling Pipeline is designed to handle new data every six hours, with updates to the AWS ODP bucket occurring daily.
Features and programs
Open Data Sponsorship Program
This dataset is part of the Open Data Sponsorship Program, an AWS program that covers the cost of storage for publicly available high-value cloud-optimized datasets.
Pricing
This is a publicly available data set. No subscription is required.
Legal
Content disclaimer
Vendors are responsible for their product descriptions and other product content. AWS does not warrant that vendors' product descriptions or other product content are accurate, complete, reliable, current, or error-free.
Delivery details
AWS Data Exchange (ADX)
AWS Data Exchange is a service that helps AWS easily share and manage data entitlements from other organizations at scale.
Open data resources
Available with or without an AWS account.
- How to use
- To access these resources, reference the Amazon Resource Name (ARN) using the AWS Command Line Interface (CLI). Learn more
- Description
- Genetic variations of SARS-CoV-2 in VCF format, organized by NCBI accession. Each VCF file corresponds to the SRA parent-run's accession ID. Files in the vcf folder are in VCF and can be read by any program that accepts *.vcf files or can read tabular data.
- Resource type
- S3 bucket
- Amazon Resource Name (ARN)
- arn:aws:s3:::sra-pub-sars-cov2
- AWS region
- us-east-1
- AWS CLI access (No AWS account required)
- aws s3 ls --no-sign-request s3://sra-pub-sars-cov2/
- Description
- Metadata for sra-pub-sars-cov2 in an Athena-queryable format
- Resource type
- S3 bucket
- Amazon Resource Name (ARN)
- arn:aws:s3:::sra-pub-sars-cov2-metadata-us-east-1
- AWS region
- us-east-1
- AWS CLI access (No AWS account required)
- aws s3 ls --no-sign-request s3://sra-pub-sars-cov2-metadata-us-east-1/
Resources
Vendor resources
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How to cite
COVID-19 Genome Sequence Dataset was accessed on DATE from https://registry.opendata.aws/ncbi-covid-19 .
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