GuidesHow do I create a new submission and upload files?

How do I create a new submission and upload files?

Creating a submission is the first step to getting your data into the AGARI platform. This guide will walk you through the process, from starting a new submission to uploading your files.

Who can create a submission?

The ability to upload data is limited to users with the appropriate permissions for a specific project. This includes the following roles:

Organisation Owner
Organisation Admin
A project-specific Admin
A project-specific Contributor

Users with a "Viewer" role cannot create submissions or upload data.

Step-by-Step Guide

The process is managed through a guided dialog.

Step 1: Start a New Submission

Navigate to the Projects page and click on the project where you want to add data.
Select the "Submissions" tab.
Click the "New Submission" button to open the dialog.

Step 2: Choose Genomic Format

The first step in the dialog is to declare how your sequence data is formatted. This is crucial for the system to correctly link your metadata to your sequences.

Single Genome FASTAs: Choose this if you have one or more FASTA files, where each file contains the sequence for a single genome (e.g., bacteria, parasites). Your metadata TSV will need a sequenceFileName column.
Multi-genome FASTAs: Choose this if you have a single FASTA file containing sequences for multiple genomes, with each record header matching an isolateId in your metadata (e.g., viruses).

Click "Next" to proceed.

Step 3: Upload Your Files

Provide a Title for your submission (e.g., "Q1 2024 Cholera Samples").
If you haven't already, download the metadata template to ensure your file is formatted correctly.
Either drag and drop your files into the upload area or click to browse your computer. You must upload one .tsv metadata file and one or more .fasta/.fa sequence files.
Once you have provided a title and uploaded a TSV file, click the "Create Submission" button.

What Happens Next?

After you create the submission, the system will process your files. A success notification will appear, and you will be automatically taken to the detail page for your new draft submission. Here, you can review the data, check for any validation errors, and publish the submission when it is ready.