Sequencing Technologies

SeqDesk includes a comprehensive sequencing technology database that facility admins can customize for their available equipment.

Technology Hierarchy

The system uses a four-level hierarchy:


Platform (e.g., Illumina NovaSeq, Oxford Nanopore MinION)
  └── Device (e.g., MinION Mk1D, PromethION 2 Solo)
       ├── Flow Cells (e.g., FLO-MIN114, FLO-PRO114M)
       ├── Kits (e.g., Ligation, Rapid, Barcoding)
       └── Software (e.g., MinKNOW, Dorado)

Admin Interface

The sequencing technology page at Admin → Sequencing Technology (/admin/sequencing-tech) has three tabs:

Platforms Tab

Manage platform-level technologies:

Edit specs, pros/cons, best use cases
Set availability status
Configure pricing indicators and turnaround times

Devices Tab

Manage specific sequencer models:

Configure device specs and features
Set compatible flow cells, kits, and software
Upload product images
Enable/disable individual devices

Accessories Tab

Manage flow cells, kits, and software:

Flow Cells — organized by category (standard, RNA, flongle, other):

Chemistry type and pore count
Maximum output capacity

Kits — organized by category:

Ligation, Rapid, Barcoding, PCR, cDNA, Direct-RNA, Amplicon
Input type and multiplexing capability

Software — organized by category:

Control software, basecalling, and analysis tools
Version tracking and download URLs

Enable/Disable

Each item has an available toggle:

Enabled — shown in order forms for researchers to select
Disabled — hidden from user-facing forms

This lets you configure only the technologies your facility actually supports.

Order Form Integration

When a sequencing-tech field is included in the order form (via Form Builder), researchers step through:

Select Platform
Select Device (auto-skipped if only one option)
Select Flow Cell (filtered by device compatibility)
Select Kit (filtered by device and category)
View compatible software (informational)

Default Data

SeqDesk ships with pre-seeded data for major platforms. Admins can:

Reset to defaults if local changes need to be reverted
Check for remote updates to sync with the latest instrument data
Apply local overrides that persist across updates

Use Your Own Registry API

If your facility needs different instruments, kits, or flow cells, you can point SeqDesk to your own registry endpoint from Admin → Sequencing Technology by changing the sync URL.

SeqDesk fetches that URL with a plain GET request and expects JSON. The response may be either:


{
  "config": {
    "version": 1,
    "technologies": []
  }
}

or the raw config object directly:


{
  "version": 1,
  "technologies": []
}

Minimum Contract

At minimum, your endpoint should return:

version: integer version used for update detection
technologies: array of platform definitions

In practice, a useful registry usually also includes:

devices: sequencer models linked to a platform with platformId
flowCells: consumables referenced by device compatibleFlowCells
kits: library or sequencing kits referenced by compatibleKits
software: software referenced by compatibleSoftware
barcodeSchemes and barcodeSets: optional barcode metadata for ONT-style kit/barcode workflows

Sync Rules

The sync URL must be a valid http or https URL.
SeqDesk compares registry items by stable id.
Bump version whenever you publish upstream changes.
If an incoming item is new, SeqDesk adds it.
If an item already exists and has local overrides enabled, the local values win.
If an item already exists without local overrides, SeqDesk still preserves the local available flag while taking remote content updates.

Recommended Response Shape


{
  "version": 3,
  "technologies": [
    {
      "id": "illumina-miseq",
      "name": "MiSeq",
      "manufacturer": "Illumina",
      "shortDescription": "Small-scale benchtop sequencing platform",
      "specs": [{ "label": "Read length", "value": "2x300", "unit": "bp" }],
      "pros": [{ "text": "Good for small amplicon runs" }],
      "cons": [{ "text": "Lower throughput than NextSeq or NovaSeq" }],
      "bestFor": ["Amplicon sequencing", "Small microbial genomes"],
      "available": true,
      "order": 10
    }
  ],
  "devices": [
    {
      "id": "miseq-v3",
      "platformId": "illumina-miseq",
      "name": "MiSeq",
      "manufacturer": "Illumina",
      "productOverview": "Compact Illumina sequencer for low-throughput runs",
      "shortDescription": "Small-scale benchtop sequencer",
      "specs": [{ "label": "Output", "value": "15", "unit": "Gb" }],
      "compatibleFlowCells": ["miseq-flow-cell-v3"],
      "compatibleKits": ["miseq-reagent-kit-v3"],
      "compatibleSoftware": ["illumina-local-run-manager"],
      "available": true,
      "order": 10
    }
  ],
  "flowCells": [
    {
      "id": "miseq-flow-cell-v3",
      "name": "MiSeq Flow Cell v3",
      "sku": "MS-102-3003",
      "category": "standard",
      "available": true,
      "order": 10
    }
  ],
  "kits": [
    {
      "id": "miseq-reagent-kit-v3",
      "name": "MiSeq Reagent Kit v3",
      "sku": "MS-102-3003",
      "category": "ligation",
      "inputType": "dna",
      "available": true,
      "order": 10
    }
  ],
  "software": [
    {
      "id": "illumina-local-run-manager",
      "name": "Local Run Manager",
      "category": "control",
      "available": true,
      "order": 10
    }
  ]
}

Operational Notes

SeqDesk does not send authentication headers when syncing, so expose the endpoint on a reachable internal URL or a public read-only URL.
Keep IDs immutable once clients have synced them; changing IDs makes items look new.
If your registry is unavailable, update checks and resets from remote defaults will fail.
The researcher-facing selector uses your synced data through the local SeqDesk API, so researchers do not need direct access to your custom registry.

Public API

Registry data is also available through public API endpoints:

Pipeline registry index: GET /api/registry — see Pipeline API
Sequencing tech summary: GET /api/sequencing-tech — see Sequencing Technology API
Full sequencing tech dataset: GET /api/registry/sequencing-tech