COVID-19 PubSeq is a free and open online bioinformatics public
sequence resource with federated data using unique identifiers and
with unique metadata, such as disambiguated
Geo localisation. PubSeq comes 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.
PubSeq is not owned by anyone. There is no central authority and
there is no (single) company that owns that data or workflows. Our
goal is simply to help map the viral variants. Early identification
of variants helps with testing and treatments! COVID-19 PubSeq
accepts sequence material from all sources. In addition, PubSeq has
specific workflows for Oxford Nanopore analysis in FAST5 and FASTQ
format. If you have an Oxford Nanopore and need (free) help
analysing SARS-CoV-2 FAST5 or FASTQ data, feel free
to contact us!
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. Note that, in
general, there is no conflict also uploading your data to other
repositories, including EBI/ENA and GISAID.
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.
The repository will be maintained and expanded for the
duration of the pandemic (and beyond). To contribute data
simply upload it! To contribute code and/or workflows see
the project
repository. For more information see
the FAQ and
the paper