DNAStack COVID19 SRA Data

bam bioinformatics coronavirus COVID-19 fasta fastq genetic genomic global health life sciences long read sequencing SARS-CoV-2 vcf virus whole genome sequencing

Description

The Sequence Read Archive (SRA) is the primary archive of high-throughput sequencing data, hosted by the National Institutes of Health (NIH). The SRA represents the largest publicly available repository of SARS-CoV-2 sequencing data. This dataset was created by DNAstack using SARS-CoV-2 sequencing data sourced from the SRA. Where possible, raw sequence data were processed by DNAstack through a unified bioinformatics pipeline to produce genome assemblies and variant calls. The use of a standardized workflow to produce this harmonized dataset allows public data generated using different methodologies to be combined and compared for a more powerful global analysis of available SARS-CoV-2 data, allowing researchers rapid access to aggregated downstream results for accelerated insight generation. Methodology: Reads from the SRA were extracted in FASTQ format, then entered into a different pipeline depending on the sequencing technology used to create the reads: the ARTIC protocol for Oxford Nanopore-derived reads; the SIGNAL pipeline for paired-end Illumina reads; and the CoSA pipeline (using DeepVariant for variant calling) for PacBio reads. Briefly, reads were primer-trimmed and aligned to the SARS-CoV-2 reference genome, following which contiguous regions were assembled and variant sites were called. Pangolin was then used to assign viral lineage based on the assembled genome.

Update Frequency

Rolling

License

DNAstack terms of use

Documentation

https://github.com/DNAstack/dnastack-open-data

Managed By

DNAstack

See all datasets managed by DNAstack.

Contact

DNAstack

How to Cite

DNAStack COVID19 SRA Data was accessed on DATE from https://registry.opendata.aws/dnastack-covid-19-sra-data.

Usage Examples

Tutorials
Tools & Applications

Resources on AWS

  • Description
    SARS-CoV-2 raw sequencing and output data (FASTQ, BAM, FASTA, VCF)
    Resource type
    S3 Bucket
    Amazon Resource Name (ARN)
    arn:aws:s3:::dnastack-covid-19-sra-data
    AWS Region
    us-west-2
    AWS CLI Access (No AWS account required)
    aws s3 ls --no-sign-request s3://dnastack-covid-19-sra-data/
    Explore
    Browse bucket

Edit this dataset entry on GitHub

Tell us about your project

Home