Creating Studies
Studies group samples from one or more orders for coordinated analysis and ENA submission. Create a study when you are ready to run pipelines or submit data publicly.
Study Creation Flow
The wizard at /studies/new starts with sample selection. The steps adapt to
the enabled form-builder modules, but the default order is:
Select Samples
Choose which samples to include in the study first:
- Browse unassigned samples from your orders
- Filter by order, sequencing technology, or search by name
- Select individual samples or use bulk selection
- Each sample can only belong to one study
Study Details
| Field | Required | Description |
|---|---|---|
| Title | Yes | Descriptive project title |
| Description | No | Detailed study description |
Plus any custom study-level fields configured in the form builder. The study
alias is not set here — it is only editable later from the study detail
page (the create endpoint does not accept it).
Environment Type
Shown when the MIxS module is enabled. Select the environment type (MIxS checklist) for your samples. This step is required when MIxS is enabled — the wizard will not let you continue without a selection. The choice determines which per-sample metadata fields appear next.
Sample Metadata
Shown when there are per-sample fields to fill (custom and/or MIxS):
- Metadata columns appear based on the selected checklist and custom fields
- Required fields are marked and validated (missing values surface as warnings, not hard errors)
- You can paste or import metadata for all samples at once with the Excel toolbar (download a template, fill it in, and upload to populate the table)
- Data is stored as JSON in each sample’s
checklistDatafield
Review
Confirm the study details, sample list, and metadata. The study is created
with readyForSubmission: false by default.
Study Properties
| Field | Description |
|---|---|
| Title | The main identifier shown in lists and on ENA |
| Alias | Short ID used as the ENA project alias (set when editing a study, not during creation) |
| Description | Free-text project description |
| Checklist Type | Environment type / MIxS checklist (Soil, Water, Wastewater/Sludge, etc.) |
| Study Metadata | Additional study-level metadata (JSON) |
| Notes | Internal notes with edit tracking |
The environment-type picker offers 13 options (human gut, human oral, human skin, human associated, host associated, plant associated, soil, water, wastewater/sludge, air, sediment, microbial mat/biofilm, and miscellaneous). There is no MAG / MIMAGS study checklist — assembly-and-bin metadata is handled by the submission pipeline, not the study checklist. See Study Metadata & MIxS for the full list.
Managing Samples
After creating a study, you can continue to manage its samples:
- Add samples — assign more unassigned samples from your orders
- Remove samples — unassign samples (sets their studyId back to null)
- Edit metadata — update MIxS fields in the sample table
- View linked files — see which reads are assigned to each sample
A sample can only belong to one study at a time. To move a sample between studies, remove it from the current study first.
Study Detail Page
The study detail page at /studies/[id] includes:
- Overview — study metadata, creation date, owner, internal notes
- Samples — interactive table of assigned samples with metadata editing
- Pipelines — pipeline runs launched from this study and their results