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 a web interface or REST API. COVID-19 PubSeq is also a repository for sequences with a low barrier to entry for uploading sequence data using best practices, including FAIR data. Data are published with metadata using state-of-the art standards and, perhaps most importantly, providing standardised workflows that get triggered on upload, so that results are immediately available in standardised data formats. 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. Importantly, all data is published under a Creative Commons license (CC0 or CC-BY-4.0). Anyone can take the published (GFA/RDF/FASTA) data and use it for further processing.