Revise sequences

Sequences can be corrected or updated after they have been submitted to Loculus. 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.

The process of submitting revisions is very similar to original submission. The main difference is that you must provide an accession column in the metadata file, which contains the Loculus accession number(s) assigned when the sequences were submitted originally.

Preparing the metadata file

The metadata file should include all the metadata fields that were originally included, both those that you wish to update and that should remain the same. (Not including a metadata column will set its value to ‘empty’.)

The metadata file should only have rows of data for the sequences in the FASTA file. It needs to include an accession column, which includes the Loculus accessions assigned at initial submission. You should also include the submissionId column, which will match the sequence names in your FASTA file.

Preparing the FASTA file

Create a FASTA file that contains only the sequences you’d like to revise, with whatever changes you’d like to make. There is no reason to edit the sequence names in the FASTA file, as long as they still match those in your metadata file.

Even if you are not revising the sequence, you must provide a FASTA file that matches the metadata file you are uploading. It should only contain the sequences that are in the metadata file (if this is fewer than your original submission), and does not otherwise need to be edited.

Submitting the revision

To submit a revision, navigate to the Submit section of the Loculus website using the link in the top-right corner of the website. Select the correct organism if requested, or ensure you’re submitting to the correct organism database via the drop-down on the top-left of the website.

Just as with an original submission, drag and drop (or select) the files where you have made the appropriate revisions. Press ‘Submit’.

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 releasing them. Once released, these changes will appear in the database after a few minutes, with the version numbers incremented.