dnastack-covid-19-sra-data.yaml

Name: DNAStack COVID19 SRA Data
Description: >
  The [Sequence Read Archive (SRA)](https://www.ncbi.nlm.nih.gov/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](https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html) for Oxford Nanopore-derived reads; the [SIGNAL pipeline](https://github.com/jaleezyy/covid-19-signal) for paired-end Illumina reads; and the [CoSA pipeline](https://github.com/PacificBiosciences/CoSA) (using [DeepVariant](https://github.com/google/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](https://github.com/cov-lineages/pangolin) was then used to assign viral lineage based on the assembled genome.
Documentation: https://github.com/DNAstack/dnastack-open-data
Contact: "[DNAstack](bioinformatics@dnastack.com)"
ManagedBy: "[DNAstack](https://dnastack.com/)"
UpdateFrequency: Rolling
Tags:
  - aws-pds
  - bam
  - bioinformatics
  - coronavirus
  - COVID-19
  - fasta
  - fastq
  - global
  - genetic
  - genomic
  - health
  - life sciences
  - long read sequencing
  - SARS-CoV-2
  - vcf
  - virus
  - whole genome sequencing
License: "[DNAstack terms of use](https://dnastack.com/terms-of-use/)"
Resources:
  - Description: SARS-CoV-2 raw sequencing and output data (FASTQ, BAM, FASTA, VCF)
    ARN: arn:aws:s3:::dnastack-covid-19-sra-data
    Region: us-west-2
    Type: S3 Bucket
    RequesterPays: False
    Explore:
      - "[Browse bucket](https://dnastack-covid-19-sra-data.s3.amazonaws.com/)"
DataAtWork:
  Tutorials:
    - Title: "Viral lineage assignment"
      URL: https://github.com/DNAstack/dnastack-open-data/tree/master/tutorials/assign_lineage
      AuthorName: "Heather Ward"
      Services:
        - Batch
        - EC2
        - S3
  Tools & Applications:
    - Title: "Viral AI"
      URL: https://viral.ai/collections/ncbi-sra-covid
      AuthorName: DNAstack