Researcher Quickstart

Register your account

Go to /register and fill in the form:

If your facility enabled the Account Validation module with enforcement on, registration from an unapproved email domain is rejected with Registration is restricted to email addresses from: …. Use your institutional address.

Then sign in at /login. You land on the Sequencing Orders page.

Create a sequencing order

From Sequencing Orders, start a new order. The wizard builds its steps from your facility’s form configuration; the shipped default gives you four:

1. Sequencing Order Details

2. Sequencing Information

3. Samples — always present. See the next step.

4. Review — a summary of your contact details, every order-level answer, and the sample table.

Your admin may have added steps (billing codes, funding details) or enabled the MIxS metadata module, which inserts a Sample Metadata step for choosing an environment checklist. A Facility Fields step exists in some installs but is never shown to you.

Add samples

The Samples step is an editable table, one row per sample. The shipped per-sample fields are:

Each row also gets an internal identifier of the form S-<timestamp>-<random>. That is what appears in file-assignment screens and, later, in the ENA submission.

For anything larger than a handful of samples, use the toolbar above the table:

1. Excel Template downloads an .xlsx workbook whose columns match the per-sample fields your facility configured.
2. Fill it in offline.
3. Upload Excel reads it back (.xlsx and .xls only — there is no CSV path), shows a validation summary, and lets you replace or append to the current rows.

For environmental samples, use metagenome organism terms — “soil metagenome”, “gut metagenome” — rather than the host species.

Review and submit

The Review step summarises everything. Read the sample table one more time, because this is a one-way door: finishing the wizard creates the order, saves the samples and submits it in a single action.

The order gets a number in the format ORD-YYYYMMDD-XXXX and lands on SUBMITTED. From that moment:

• Sample rows can no longer be added, edited or removed. The API answers Cannot modify samples after order submission.
• The order can no longer be deleted by you. The API answers Cannot delete order after submission.
• Order-level metadata (name, contact, library settings) stays editable until the order reaches COMPLETED.
• You cannot change the status again. SUBMITTED → anything returns Invalid status transition for a researcher.

Ship the samples and mark them sent

After submission the order page shows a Sequencing Order Process panel with three steps:

1. Sequencing Order Submitted — done.
2. Send Samples to Institutions — your facility’s shipping instructions appear here (your admin writes them), along with a Mark sent button. Press it once the physical samples are on their way. It records a note the facility can see, and it can only be pressed once.
3. Waiting for Sequencing — flips to done when every sample has a file.

Track progress

The order’s status tells you where you are:

COMPLETED is usually set automatically: as soon as the last sample gets a file, SeqDesk flips the order and writes the note “Automatically completed - all samples have sequencing files”.

Your facility can also add free-text status notes, visible on the order detail page, and you will get in-app notifications when your order is created or updated.

Group samples into a study

You do not have to wait for sequencing to finish. Create a study from Studies, give it a title and description, choose a MIxS checklist if your facility uses them, and assign your samples.

Two things to know:

• A sample belongs to at most one study. Assigning it to a second study moves it out of the first.
• A study can draw samples from several sequencing orders. That is the point — the order is administrative, the study is scientific. But every sample you assign has to come from an order you own; anything else is rejected with Cannot assign samples you don't own.

The study description becomes the public <DESCRIPTION> of the ENA project, so write it for a stranger. When the metadata is complete, mark the study ready for submission; the facility takes it from there.

Collect your data

Two separate publication gates stand between finished work and your download button, and both are pressed by a facility admin:

Sequencing files. Attaching a FASTQ file to your sample does not make it visible to you. An admin has to press Make downloadable to user on the order. Until then, the delivery endpoint answers Sequencing files are not available for this sequencing order. Once published, you see only reads the facility has classified as cleaned — raw or unclassified reads are never delivered — plus any reports the facility marked as customer-facing.

Analysis results. A completed pipeline run is invisible to you until an admin marks it Final for that pipeline on your study or order. Exactly one run can be final per pipeline per target, so if the facility re-runs an analysis and marks the new run final, it replaces the old one in your view.

If your order says COMPLETED but Analysis is empty and there is nothing to download, the work is done and simply not published yet. Ask the facility.