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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. For more information see the FAQ!.

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Make your sequence data FAIR. Upload your SARS-CoV-2 sequence (FASTA or FASTQ formats) with simple metadata (JSONLD) to the public sequence resource. The upload will trigger a recompute with all available sequences into a Pangenome available for download!

Your uploaded sequence will automatically be processed and incorporated into the public pangenome with metadata using worklows from the High Performance Open Biology Lab defined here. All data is published under a Creative Commons license You can take the published (GFA/RDF/FASTA) data and store it in a triple store for further processing. Clinical data can be stored securely at REDCap.

Data can be uploaded from any sequencing platform in FASTA format. We give special attention to workflows for the Oxford Nanopore - see also pubmed - because it offers an affordable platform that is great for SARS-CoV-2 sequencing and identification. In New Zealand the Oxford Nanopore is used for all tracing.

Note that form fields contain web ontology URI's for disambiguation and machine readable metadata. For examples of use, see the docs.

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