PubSeq - Public Sequence Resource

Stream data with DDA:

from dagshub.streaming import DagsHubFilesystem

fs = DagsHubFilesystem(".", repo_url="https://dagshub.com/DagsHub-Datasets/pubseq-dataset")

fs.listdir("s3://pubseq-datasets")

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.

Contact:

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.

Managed By:

https://covid19.genenetwork.org/

Resources:

1. resource:
   • Description: PubSeq submitted datasets (FASTA and JSON metadata)
   • ARN: arn:aws:s3:::pubseq-datasets
   • Region: us-east-2
   • Type: S3 Bucket
   • Explore: Browse Bucket
2. resource:
   • Description: Pubseq output data (Arvados Keep)
   • ARN: arn:aws:s3:::pubseq-output-data
   • Region: us-east-2
   • Type: S3 Bucket
   • Explore: Arvados download

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

Tutorials:

1. tutorial:

   • Title: PubSeq FAQ
   • URL: https://covid19.genenetwork.org/about
   • AuthorName: PubSeq development team
   • AuthorURL: https://github.com/pubseq

2. tutorial:

   • Title: PubSeq Documentation
   • URL: https://covid19.genenetwork.org/blog
   • AuthorName: PubSeq development team
   • AuthorURL: https://github.com/pubseq

3. tutorial:

   • Title: Query metadata
   • URL: https://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part1
   • AuthorName: PubSeq development team
   • AuthorURL: https://github.com/pubseq

4. tutorial:

   • 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

5. tutorial:

   • Title: REST API
   • URL: https://covid19.genenetwork.org/apidoc
   • AuthorName: PubSeq development team
   • AuthorURL: https://github.com/pubseq

Tools & Applications:

1. 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

2. tools & applications:

   • 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

3. tools & applications:

   • 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

Publication:

1. publication:
   • 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.