Samples & Metadata
Samples are the core data unit in SeqDesk. Each sample belongs to an order and can optionally be assigned to a study for analysis and ENA submission.
Default Sample Fields
Every sample has these system-level fields that are always present:
| Field | Type | Description |
|---|---|---|
sampleId | Auto | Internal identifier (S-{timestamp}-{random}), read-only |
scientificName | Text | Taxonomic name, set via the Organism autocomplete |
taxId | Text | NCBI Taxonomy ID, auto-filled from organism search |
sampleAlias | Text | User-friendly short name, auto-generated if empty |
These fields are managed by SeqDesk and stored directly on the Sample record in the database.
Default Per-Sample Form Fields
The order wizard includes these per-sample columns by default:
| Column | Required | Description |
|---|---|---|
| Organism | Yes | NCBI taxonomy lookup — start typing a name to search |
| Sample Title | Yes | A short descriptive title (used for ENA submission) |
| Sample Alias | No | Optional unique identifier |
Your facility admin can add more per-sample columns (e.g. sample volume, concentration, barcodes, or any custom metadata) through the Form Builder. The columns you see in the sample table depend on your facility’s configuration.
MIxS Metadata
MIxS (Minimum Information about any Sequence) is a standard for describing sequencing samples. When a MIxS checklist is selected for an order or study, additional metadata columns appear in the sample table.
MIxS fields are stored as JSON in the checklistData field. Units for numeric
fields are stored separately in checklistUnits.
Common checklist types include:
- MAG (Metagenome-Assembled Genome)
- Wastewater
- Soil
- Environmental
- Host-associated
The required fields vary by checklist type and are important for ENA submission.
Editing Samples
Table Editing
The sample table supports:
- Keyboard navigation — arrow keys, Tab, Enter to move between cells
- Inline editing — click a cell to edit it directly
- Organism autocomplete — type a name to search NCBI taxonomy
- Add rows — add blank rows at the bottom
- Delete rows — remove rows (DRAFT orders only)
- Undo — revert unsaved changes
Excel Import/Export
For bulk editing:
- Export the sample table to Excel — downloads a spreadsheet with current data
- Edit in your spreadsheet application — add rows, fill in data
- Import the spreadsheet back — columns are matched by header name
This is the fastest way to add many samples with metadata.
Custom Fields
If the admin has configured per-sample custom fields in the
Form Builder, they appear as additional
columns in the sample table. Custom field data is stored as JSON in the
customFields field.
Sample Lifecycle
Created in Order (DRAFT)
→ Order submitted
→ Assigned to Study (optional)
→ Files assigned (Reads linked)
→ Pipeline run (Assemblies, Bins created)
→ ENA submission (Accession numbers assigned)Key Relationships
- Order — every sample belongs to exactly one order (required)
- Study — a sample can be assigned to one study (optional)
- Reads — sequencing files linked to the sample
- Assemblies — pipeline output assemblies
- Bins — genome bins from binning pipelines