Upload your SARS-CoV-2 sequence (FASTA or FASTQ formats) with 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 4.0 attribution license (CC-BY-4.0). You can take the published (GFA/RDF/FASTA) data and store it in a triple store for further processing. We also plan to combine identifiers with clinical data stored securely at REDCap. A free command line version of the uploader can be installed from source.

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

Upload SARS-CoV-2 Sequence

Select FASTA file of assembled genome (form upload max 50K; FASTQ and BAM is coming soon):

Note that by uploading your data you automatically agree to a CC-BY-4.0 license.

Select metadata submission method:
Fill in metadata manually Upload metadata file
Make sure the metadata has submitter attribution details.

Select JSON or YAML metadata file following this schema and example (max 50K):

{% for record in fields %} {% if 'heading' in record %} {% if loop.index > 1 and 2 < 3 %}

{% endif %}

{% else %}

{{ record['label'] }} {{ "*" if record['required'] else "" }} {% if 'docstring' in record %} ❓ {% endif %} {% if 'ref_iri' in record %} 🔗 {% endif %} {% if record['type'] == 'select' %} {% else %} {% endif %}

{% if record['list'] %} {% endif %}

{% endif %} {% if loop.index == loop.length %}

{% endif %} {% endfor %}

ABOUT

This a public repository created at the COVID-19 BioHackathon that has a low barrier to entry for uploading sequence data using best practices. I.e., data is published with a creative commons 4.0 (CC-4.0) license with metadata using state-of-the art standards and, perhaps most importantly, providing standardized workflows that get triggered on upload, so that results are immediately available in standardized data formats. The repository will be maintained and expanded for the duration of the pandemic. To contribute data simply upload it! To contribute code and/or workflows see the project repository. For more information see the paper (WIP).

Upload SARS-CoV-2 Sequence

{{ record['heading'] }}

ABOUT