Once you’ve uploaded sequences via the website or API, you will have to approve them before they are fully submitted.
After submitting sequences, you’ll be taken to a page showing the progress of processing every sequence. For each sequence, it will show whether its awaiting processing, being processed, or has finished processing.
Sequences that have finished processing will show different icons to indicate whether there were any issues during the processing.
We highly recommend checking all sequences with warnings to see if they could be rectified or indicate a larger problem with the data.
You can only approve and release sequences that have yellow or green checkmarks (no warnings or errors, or only errors) - you cannot approve and release sequences with errors.
You can filter the processed sequences to only show those with warnings, errors, or which passed, to help you decide which actions to take.
If see something you’d like to change, or want to try and resolve a warning, you can edit the sequence.
For each sequence, you have 3 options (2 if the sequence has an error), indicated to the right: release (paper plane), edit (pencil and paper), and discard (waste bin). Clicking on any of these icons for one sequence, will execute the action on that sequence only. When you release or discard a sequence, it will no longer be shown on the page.
You can also take action on multiple sequences at once, using the buttons above the displayed sequences.
Discarding: You can choose to discard either all sequences, or those with errors. If you discard all sequences, you will need to start the submission process over.
Releasing: You can release all valid sequences (those without warnings or errors, and those with warnings), leaving only those with errors.
Once you release your sequences, they will appear on Pathoplexus within a couple minutes.
If you leave any sequences unreleased, you can view, edit, and approve/release (if they have no errors) them at a later time.
You can also always view your released sequences by going to ‘Browse’ in the top-right menu, then selecting the pathogen, then clicking ‘View’.
Instructions coming soon. See the Swagger API documentation