Sequencing Orders & Samples
A Sequencing Order is the record of one sequencing request: who asked for it, which samples are involved, what should be run on them, and — once the facility is done — which files came back. Everything else in SeqDesk hangs off it. Samples cannot exist without an order, sequencing runs are created inside an order, and read files are linked to samples that belong to an order.
Naming. The database model is Order and its identifiers are
orderId / orderNumber (ORD-YYYYMMDD-XXXX), but the interface calls it a
Sequencing Order. A SequencingRun is a different thing — the physical
run on an instrument. One Sequencing Order contains zero or more Sequencing
Runs. See Sequencing Runs.
The mental model
Read this once and the rest of the section follows:
Sequencing Order (ORD-20260415-0001, status DRAFT → SUBMITTED → COMPLETED)
├── Sample (S-1755262041412-K7QX2, one per tube)
│ ├── Read (file1 / file2 — the FASTQ pair linked to this sample)
│ ├── Assembly / Bin (produced later by pipelines)
│ └── Study (optional, at most one — the analysis / publication grouping)
└── SequencingRun (the instrument run; maps barcodes → samples)Three facts that explain most of SeqDesk’s behaviour:
- A sample belongs to exactly one order, forever.
Sample.orderIdis required and is never reassigned. If a tube was ordered under the wrong order, the sample has to be recreated. - A sample belongs to at most one study.
Sample.studyIdis nullable. Studies are how you regroup samples across orders for analysis and ENA submission — see Studies. - Reads are attached to samples, not to orders or runs. A
SequencingRunrecords the barcode plan; the actual FASTQ paths live onReadrecords pointing at samples.
Who does what
SeqDesk has two roles that matter here, and the split is strict.
Researcher (RESEARCHER) | Facility admin (FACILITY_ADMIN) | |
|---|---|---|
| Create a sequencing order | Yes | Yes |
| Edit sample data (organism, titles, MIxS, custom fields) | Only while DRAFT | Only while DRAFT |
| Edit order-level metadata | Until COMPLETED | Always |
| Edit admin-only fields (Internal QC Status, Sample QC Result, …) | Never — they are invisible | Always |
| Create sequencing runs and run plans | Never | Once SUBMITTED |
| Discover, associate and upload read files | Never | Once SUBMITTED |
| See the read files at all | Only after the facility publishes them | Always |
| Delete a submitted order | Never | Only if the admin setting allows it |
That last row is the one people trip over: until a facility admin presses Make downloadable to user, a researcher’s order page shows no read files at all, even though the files are linked in the database. See Sequencing Order Lifecycle.
Where to start
- New researcher? Read Creating Sequencing Orders, fill in the wizard, submit, then watch the three-step Sequencing Order Process panel on the order page.
- New facility admin? Read Sequencing Order Lifecycle for the status rules, then Sequencing Runs to set up a run plan before the data arrives — it makes file matching far more reliable.
- Data has arrived and nothing matches? Go straight to File Discovery and Assigning Files to Samples.
Related sections
- Studies — regrouping samples for analysis and ENA submission.
- Pipelines & Analysis — running Nextflow workflows against an order’s linked reads or a study’s samples.
- Administration → Form Builders — adding, hiding and reordering the fields that appear in the order wizard.
- Administration → Data Storage — the data directory that file discovery scans.