About/FAQ

The public sequence resource aims to provide a generic and useful resource for COVID-19 research. The focus is on providing the best possible sequence data with associated metadata that can be used for sequence comparison and protein prediction.

The public sequence resource is an initiative by bioinformatics and ontology experts who want to create something agile and useful for the wider research community. The initiative started at the COVID-19 biohackathon in April 2020 and is ongoing. The main project drivers are Pjotr Prins (UTHSC), Peter Amstutz (Curii), Michael Crusoe (Common Workflow Language), Thomas Liener (consultant, formerly EBI) and Jerven Bolleman (Swiss Institute of Bioinformatics).

Notably, as this is a free software initiative, the project represents major work by hundreds of software developers and ontology and data wrangling experts. Thank you everyone!

The short version is that we use state-of-the-art practices in bioinformatics using agile methods. Unlike the resources from large institutes we can improve things on a dime and anyone can contribute to building out this resource!

Importantly: all data is published under the Creative Commons 4.0 attribution license which means it data can be published and workflows can run in public environments allowing for improved access for research and reproducible results. This contrasts with some other public resources, including GISAID.

1. We champion truly shareable data without licensing restrictions - with proper attribution
2. We provide full metadata support using state-of-the-art ontology's
3. We provide a web-based sequence uploader and a command-line version for bulk uploads
4. We provide a live SPARQL end-point for all metadata
5. We provide free data analysis and sequence comparison triggered on data upload
6. We provide free downloads of all computed output
7. There is no need to set up pipelines and/or compute clusters
8. All workflows get triggered on uploading a new sequence
9. When someone (you?) improves the software/workflows and everyone benefits
10. Your data gets automatically integrated with the Swiss Institure of Bioinformatics COVID-19 knowledge base https://covid-19-sparql.expasy.org/ (Elixir Switzerland)

Finally, if you upload your data here we have workflows that output formatted data suitable for uploading to EBI resources (and soon others). Uploading your data here get your data ready for upload to multiple resources.

Funny question. There is no good reason not to upload your data here! In fact, you can upload your data here as well as to other resources. It is your data after all. No one can prevent you from uploading your data to multiple resources. We recommend uploading to EBI and NCBI resources. Use our data conversion tools to only enter data once and make the process smooth.

On uploading a sequence with metadata it will automatically be processed and incorporated into the public pangenome with metadata using workflows from the High Performance Open Biology Lab defined here.

All data is published under a Creative Commons 4.0 attribution license (CC-BY-4.0). You can download the raw and published (GFA/RDF/FASTA) data and store it for further processing.

Absolutely. Free software allows for fully reproducible pipelines. You can take our workflows and data and run it elsewhere!

We are preparing raw sequence data pipelines (fastq and BAM). The reason is that we want the best data possible for downstream analysis (including protein prediction and test development). The current approach where people publish final sequences of SARS-CoV-2 is lacking because it hides how this sequence was created. For reasons of reproducible and improved results we want/need to work with the raw sequence reads (both short reads and long reads) and take alternative assembly variations into consideration. This is all work in progress.

See the http://covid19.genenetwork.org/blog!

See the http://covid19.genenetwork.org/blog!

Go to our source code repositories, fork/clone the repository, change something and submit a pull request (PR). That easy! Check out how many PRs we already merged.

A public sequence resource is about public data. Metadata can refer to private data. You can use your own (anonymous) identifiers. We also plan to combine identifiers with clinical data stored securely at REDCap. See the relevant tracker for more information and contributing.

The main sponsors are listed in the footer. In addition to the time generously donated by many contributors we also acknowledge Amazon AWS for donating COVID-19 related compute time.