Automated GISAID submissions

Sequencing sites can opt-in to a process where consensus sequences uploaded to CLIMB that pass high quality QC are automatically submitted to GISAID on their behalf.

How do I opt-in?

You can opt-in via your Institute profile on Majora. One only user per site needs to provide this information and it does not need to be the same person who provides the metadata or uploads the sequences. You will need to provide:

• your e-mail address (we will pass this on to GISAID curators to contact you about your entries)
• a valid GISAID username (if you have not registered, you will need to get a GISAID account first), this username is not your email address, failing to provide the username for your account will cause errors for your submissions
• the name of the lab or labs that you wish to credit as the originating lab (this will include your sequencing lab)
• a list of people you wish you credit

You will also need to contact GISAID and let them know you wish to allow the COG-UK consortium user to submit sequences on your behalf.

How does it work?

Bulk uploads are automatically generated at 12:30 (BST, not adjusted during winter) every working day (Mon - Fri) and will release all new seqeunces that passed high quality QC. Samples are uploaded 3 days after they are ingested into the CLIMB-COVID dataset.

Do I have to do anything?

You should periodically check the “My Unreleased” tab on the GISAID website. Curators will flag sequences with frameshifts and other quality artefacts for you to approve before they are made public, we do not control this process.

CHANGELOG

• 2023-09-06: Upload lag changed to 3 days, down from >7 days.

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Published 2020-04-15. Updated 2022-01-14. Page maintainer @samstudio8.