Name: PubSeq - Public Sequence Resource
License: Creative Commons Attribution 4.0 International (CC BY 4.0) unless otherwise specified.

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

How to Cite

PubSeq - Public Sequence Resource was accessed on DATE from https://registry.opendata.aws/pubseq.

Usage Examples

Tutorials

Tools & Applications

Publications

Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 during Border Quarantine and Air Travel, New Zealand (Aotearoa) by Eichler, N. et al.

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 --no-sign-request s3://pubseq-datasets/

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 --no-sign-request s3://pubseq-output-data/

Explore

Arvados download