You must create an account and be logged into Pathoplexus to create SeqSets (pronounced seek-sets).
On the top-right corner of Pathoplexus, click on the ‘SeqSets’ link.
Any SeqSets you’ve created previously will be shown in a table.
New SeqSets can be created by clicking on the + icon next to the ‘SeqSets’ heading.
After clicking the +, a new box will open allowing you to name and describe the SeqSet, and to add accession numbers.
You can add accession numbers to be part of your Focal and Background datasets - definitions of what these are how to use them correctly
(as set out in the Data Use Terms) can be found in the Data Use Terms under Publications and Preprints.
You can currently only add Pathoplexus accession numbers. These can be added with or without the version.
After adding all your accessions, click ‘Save’ to generate a new SeqSet.
SeqSets can be shared via the URL visible when viewing a SeqSet page. Simply copy this from your browser and others will be able to use this link to view your SeqSet (without needing a Pathoplexus account).
If you generate a DOI for the SeqSet (see below), you can also share this link.
You can add a DOI in order to reference the SeqSet more easily, and to allow your SeqSet to be referenced in publications.
Important: Note that after generating at DOI, you will not be able to edit that SeqSet directly any longer. If you make edits, you will generate a new ‘version’ of the SeqSet, which will require generating a new DOI. For this reason, we suggest finalizing your list of sequences before generating a DOI.
After generating a SeqSet, click on it to view an overview. Next to ‘DOI’ you’ll see a link to “Generate a DOI”. Press this, confirm you really want to create a DOI, and a DOI will be automatically generated.
It can take up to a day for your DOI to be registered in the system and for the provided link to work correctly.
If you edit a SeqSet after generating a DOI, you will need to generate a new DOI. Thus, it’s usually better to wait until you are confident that you have pulled together all the sequences you want to reference, before generating a DOI.
Once you have generated a DOI, you can no longer delete a SeqSet, as DOIs are intended to be persistent.
You can edit a SeqSet by selecting it and then clicking the ‘Edit’ button on the top of the page.
When you edit a SeqSet, you will generate a new version of that SeqSet, which will be visible when you return to your SeqSet overview page.
If you edit a SeqSet after generating a DOI, you will need to generate a new DOI. Thus, it’s usually better to finalize your set of sequences before generating a DOI.
You can use the ‘Export’ button when viewing a SeqSet, to export information about that SeqSet (including the accessions of the sequences included in the SeqSet) into JSON or TSV format.
You can also generate citation information in BibTeX, MLA, and APA style.
You can only delete SeqSets that do not have DOIs. To do this, click on the SeqSet and click the ‘Delete’ button.
Note that deletion is permanent and people will no longer be able to view this SeqSet.