COVID-19 Genome Sequence Dataset

Stream data with DDA:

from dagshub.streaming import DagsHubFilesystem

fs = DagsHubFilesystem(".", repo_url="https://dagshub.com/DagsHub-Datasets/ncbi-covid-19-dataset")

fs.listdir("s3://sra-pub-sars-cov2")

Description:

A centralized sequence repository for all records containing sequence associated with the novel corona virus (SARS-CoV-2) submitted to the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). Included are both the original sequences submitted by the principal investigator as well as SRA-processed sequences that require the SRA Toolkit for analysis. Additionally, submitter provided metadata included in associated BioSample and BioProject records is available alongside NCBI calculated data, such k-mer based taxonomy analysis results, contiguous assemblies (contigs) and associated statistics such as contig length, blast results for the assembled contigs, contig annotation, blast databases of contigs and their annotated peptides, and VCF files generated for each record relative to the SARS-CoV-2 RefSeq record. Finally, metadata is additionally made available in parquet format to facilitate search and filtering using the AWS Athena Service.

Contact:

A centralized sequence repository for all records containing sequence associated with the novel corona virus (SARS-CoV-2) submitted to the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). Included are both the original sequences submitted by the principal investigator as well as SRA-processed sequences that require the SRA Toolkit for analysis. Additionally, submitter provided metadata included in associated BioSample and BioProject records is available alongside NCBI calculated data, such k-mer based taxonomy analysis results, contiguous assemblies (contigs) and associated statistics such as contig length, blast results for the assembled contigs, contig annotation, blast databases of contigs and their annotated peptides, and VCF files generated for each record relative to the SARS-CoV-2 RefSeq record. Finally, metadata is additionally made available in parquet format to facilitate search and filtering using the AWS Athena Service.

Update Frequency:

Hourly

Managed By:

NLM

Resources:

1. resource:

   • Description: Genomic sequence reads of SARS-CoV-2 and related coronaviridae, organized by NCBI accession. Files in the sra-src folder are in FASTQ, BAM, or CRAM format (original submission); files in the run folder are in .sra format and require the SRA Toolkit
   • ARN: arn:aws:s3:::sra-pub-sars-cov2
   • Region: us-east-1
   • Type: S3 Bucket

2. resource:

   • Description: Metadata for sra-pub-sars-cov2 in an Athena-queryable format
   • ARN: arn:aws:s3:::sra-pub-sars-cov2-metadata-us-east-1
   • Region: us-east-1
   • Type: S3 Bucket

Tags:

aws-pds, bioinformatics, biology, coronavirus, COVID-19, fastq, bam, cram, genomic, genetic, health, life sciences, MERS, SARS, virus, STRIDES, whole genome sequencing, transcriptomics

Tools & Applications:

1. tools & applications:
   • Title: Download SRA sequence data using Amazon Web Services (AWS)
   • URL: https://www.ncbi.nlm.nih.gov/sra/docs/sra-aws-download/
   • AuthorName: NCBI SRA