PubSeq - Public Sequence Resource

bam bioinformatics biology coronavirus COVID-19 fast5 fasta fastq genetic genomic health json life sciences long read sequencing medicine MERS metadata open source software RDF SARS SARS-CoV-2 SPARQL

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.

Update Frequency

Rolling dataset.

License

Creative Commons Attribution 4.0 International (CC BY 4.0) unless otherwise specified.

Documentation

https://covid19.genenetwork.org/about

Managed By

UTHSC GeneNetwork

See all datasets managed by UTHSC GeneNetwork.

Contact

https://covid19.genenetwork.org/contact

Usage Examples

Tutorials
Tools & Applications
Publications

Resources on AWS

  • Description
    PubSeq submitted datasets (FASTA and JSON metadata)
    Resource type
    S3 Bucket
    Amazon Resource Name (ARN)
    arn:aws:s3:::pubseq-datasets
    AWS Region
    us-east-2
    AWS CLI Access (No AWS account required)
    aws s3 ls s3://pubseq-datasets/ --no-sign-request
    Explore
    Browse Bucket
  • Description
    Pubseq output data (Arvados Keep)
    Resource type
    S3 Bucket
    Amazon Resource Name (ARN)
    arn:aws:s3:::pubseq-output-data
    AWS Region
    us-east-2
    AWS CLI Access (No AWS account required)
    aws s3 ls s3://pubseq-output-data/ --no-sign-request
    Explore
    Arvados download

Edit this dataset entry on GitHub

Home