Sequences can be corrected or updated after they have been submitted to Pathoplexus. Submitting these changes (“revisions”) will cause the version of the sequence to be incremented, and previous versions of the metadata and sequence data can always be accessed via previous version numbers. (See Versioning)
You can revise sequences via the website (particularly good for a small number of sequences and relatively simple edits), or by reuploading updated files (good for large numbers of sequences, or more extensive revisions - but requires the original data files that were submitted, see docs below on how to download the original data from Loculus!)
The easiest way to revise your sequences, especially for a small number of sequences, is to edit them directly on the Pathoplexus website. Here’s how:
On the revision page, you can:
You’ll then be taken to a review page similar to the initial submission dialog. This page shows all sequences for which you’ve made revisions.
Important: Before your changes are made visible in the database, you must click ‘Approve valid sequences’ - this is the same as with initial submissions, and without it, the changes will not take effect.
You can approve changes immediately as you revise sequences one by one, or you can revise multiple sequences and then approve them all together.
Submitting revisions using modified files is very similar to making an original submission.
The main difference is that revision metadata must include an accession column containing the Pathoplexus accession assigned during the original submission.
Important: The accession column should contain the accession without the version number. For example, use PP_0049AAG rather than PP_0049AAG.1. (See Accessions for more information on accession format.)
Whenever possible, use the original metadata and sequence files from your initial Pathoplexus submission as the starting point for your revision. You can either use your own copies of these files or download them from Pathoplexus.
The easiest way to prepare revision files is to download your original submission data:
Pathoplexus automatically adds the required accession column to downloaded metadata.
Alternatively, if you already have the original submission files, you can edit those directly. Add an accession column to the metadata file containing the Pathoplexus accessions assigned during the original submission.
Your revision upload must always include:
For single-segmented organisms, FASTA sequence IDs must match the values in the metadata id column.
For multi-segmented organisms, include a fastaIds column in the metadata file containing a space-separated list of all FASTA IDs linked to each metadata entry.
We encourage you to add a short description of your changes in the optional versionComment metadata field explaining the reason for the revision.
To revise metadata, edit the relevant fields in your metadata file. The metadata file should include all the metadata fields that were originally included, both those that you wish to update and those that should remain the same. (Not including a metadata column will set its value to ‘empty’.)
The FASTA file does not need to be modified if the sequences are unchanged, but you must still include a matching FASTA file when submitting the revision.
To revise sequences, edit the relevant sequences in the FASTA file.
The sequence IDs do not need to be changed as long as they still match the corresponding metadata entries (id for single-segmented organisms or fastaIds for multi-segmented organisms).
You can also revise metadata fields at the same time by editing the metadata file.
By default, revising the metadata or sequence data will not affect the raw reads files attached to your submissions. The Download original data metadata file is prepropulated with a files.rawReads column that links each entry to your already-uploaded files. This means that if you don’t want to update the raw reads data of your submission you do not need to re-upload the raw reads files and do not need to perform any additional action besides making the metadata or sequence edits you want; just ensure that you leave the files.rawReads column exactly as it was when you downloaded the original data.
If you do want to change the raw reads files associated with your submission, you will need to edit the files.rawReads column in the metadata file according to the instructions below:
files.rawReads field (see here for a detailed description), and upload the file via the ‘Upload folder’ or ‘Upload files’ functionality during submission.files.rawReads field and remove the name of the file you wish to delete. The name will be shown as name:fileId, where fileId is the internal accession Pathoplexus assigned to the file. Please ensure to remove to full name:fileId entry from your metadata file in order to delete the raw reads.name:fileId of the file you want to replace, replace it with the new file name, and upload the corresponding file via the ‘Upload folder’ or ‘Upload files’ functionality during submission.To submit a revision, navigate to the Submit section of the Pathoplexus website using the link in the top-right corner of the website.
Select the correct pathogen if requested, or ensure you’re submitting to the correct pathogen database via the drop-down on the top-left of the website.
When on the page with ‘Submit’, ‘Revise’, ‘Review’, and ‘View’ boxes, select ‘Revise’.
Just as with an original submission, drag and drop (or select) the files where you have made the appropriate revisions. Ensure you specify the same Terms of Data as you previously chose for your sequences. Press ‘Upload and proceed to Approval’.
You will be directed to the same processing page as you’re taken to during initial submission, where you can view the sequences and their changes before approving them. Once approved, these changes will appear in the database after a few minutes, with the version numbers incremented.