aws-opendata-pubseq.yaml

# Project description file for AWS-OpenData
# See https://github.com/awslabs/open-data-registry
Name: PubSeq - Public Sequence Resource
Description: COVID-19 PubSeq is a free and open online bioinformatics public sequence resource with on-the-fly analysis of sequenced SARS-CoV-2 samples that allows for a quick turnaround in identification of new virus strains. PubSeq allows anyone to upload sequence material in the form of FASTA or FASTQ files with accompanying metadata through the web interface or REST API.
Documentation: https://covid19.genenetwork.org/about
Contact: https://covid19.genenetwork.org/contact
ManagedBy: "[UTHSC GeneNetwork](https://covid19.genenetwork.org/)"
UpdateFrequency: Rolling dataset.
Tags:
  - aws-pds
  - bam
  - bioinformatics
  - biology
  - coronavirus
  - COVID-19
  - fasta
  - fastq
  - fast5
  - genetic
  - genomic
  - health
  - json
  - life sciences
  - long read sequencing
  - open source software
  - MERS
  - metadata
  - medicine
  - RDF
  - SARS
  - SARS-CoV-2
  - SPARQL
License: Creative Commons Attribution 4.0 International (CC BY 4.0) unless otherwise specified.
Resources:
  - Description: PubSeq submitted datasets (Arvados Keep)
    ARN: arn:aws:s3:::pubseq-datasets
    Region: us-east-2
    Type: S3 Bucket
    Explore:
    - '[Arvados download](https://covid19.genenetwork.org/download)'
  - Description: Pubseq compiled metadata (Arvados Keep)
    ARN: arn:aws:s3:::pubseq-metadata
    Region: us-east-2
    Type: S3 Bucket
    Explore:
    - '[Arvados download](https://covid19.genenetwork.org/download)'
  - Description: Pubseq output data (Arvados Keep)
    ARN: arn:aws:s3:::pubseq-output-data
    Region: us-east-1
    Type: S3 Bucket
    Explore:
    - '[Arvados download](https://covid19.genenetwork.org/download)'
DataAtWork:
  Tutorials:
    - Title: PubSeq FAQ
      URL: https://covid19.genenetwork.org/about
      AuthorName: PubSeq development team
      AuthorURL: https://github.com/pubseq
    - Title: PubSeq Documentation
      URL: https://covid19.genenetwork.org/blog
      AuthorName: PubSeq development team
      AuthorURL: https://github.com/pubseq
    - Title: Query metadata
      URL: https://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part1
      AuthorName: PubSeq development team
      AuthorURL: https://github.com/pubseq
    - Title: Submitting a sequence
      URL: https://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part3
      AuthorName: PubSeq development team
      AuthorURL: https://github.com/pubseq
    - Title: REST API
      URL: https://covid19.genenetwork.org/apidoc
      AuthorName: PubSeq development team
      AuthorURL: https://github.com/pubseq
  Tools & Applications:
    - Title: Source code for website
      URL: https://github.com/pubseq/bh20-seq-resource/tree/master/bh20simplewebuploader
      AuthorName: PubSeq development team
      AuthorURL: https://github.com/pubseq
    - Title: Source code for CWL workflows
      URL: https://github.com/pubseq/bh20-seq-resource/tree/master/workflows
      AuthorName: PubSeq development team
      AuthorURL: https://github.com/pubseq
    - Title: Source code for (meta)data uploader
      URL: https://github.com/pubseq/bh20-seq-resource/tree/master/bh20sequploader
      AuthorName: PubSeq development team
      AuthorURL: https://github.com/pubseq
  Publications:
    - Title: Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 during Border Quarantine and Air Travel, New Zealand (Aotearoa)
      URL: https://wwwnc.cdc.gov/eid/article/27/5/21-0514_article
      AuthorName: Eichler, N. et al.