# LIMS for NGS

## Overview

Labii LIMS for NGS helps laboratories manage next-generation sequencing (NGS) operations with traceable, structured, and repeatable workflows. It centralizes sample receiving, extraction, library preparation, sequencing outputs, and experiment documentation in one system.

This application is designed for sequencing cores, translational research groups, biotech teams, and molecular diagnostics labs that need clear chain-of-custody and operational consistency across NGS runs. It reduces manual tracking errors and improves data integrity by connecting materials, protocols, storage, and consumption records.

Labii LIMS for NGS is built on the Labii platform and works alongside core ELN and workflow capabilities. Learn more about the Labii platform at [Laboratory Information Management System (LIMS)](https://www.labii.com/laboratory-information-management-system-lims).

### Included Tables

The LIMS for NGS template includes the following tables:

* `pj_project`
* `core_receiving`
* `ngs_sample`
* `ngs_extract`
* `ngs_library`
* `ngs_fastq`
* `eln_experiment`
* `eln_protocol`
* `core_storage`
* `core_consumption`

## Use Cases

### Centralized Sample-to-FASTQ Tracking

* Track each material state from receiving to extraction, library, and FASTQ output
* Maintain lineage between upstream materials and downstream sequencing artifacts
* Reduce gaps in documentation during handoffs between teams

### Sequencing Core Operations

* Standardize intake, accessioning, and processing workflows
* Document protocol usage and experiment execution across instruments and operators
* Improve turnaround visibility for internal and external projects

### Regulated and Quality-Focused Environments

* Preserve complete audit-ready records for sample handling and transformation
* Align operational practices with GLP/GMP-style documentation expectations
* Improve reproducibility and inspection readiness

## Getting Started

{% stepper %}
{% step %}
Go to **Settings** → **Applications**.
{% endstep %}

{% step %}
Click **Add application** and choose **Add from a template**.
{% endstep %}

{% step %}
Select **LIMS for NGS** from the template list.
{% endstep %}

{% step %}
Confirm the template installation and open the application from the side menu.
{% endstep %}

{% step %}
Optionally install **Equipment Management** to capture instrument and equipment usage with sequencing workflows.
{% endstep %}
{% endstepper %}

## Core Workflows

### Sample Receiving and Accessioning

Use this workflow to register incoming samples and ensure each item enters the NGS pipeline with complete metadata.

{% stepper %}
{% step %}
Open the **Receiving** table and add a new receiving record for the incoming shipment or sample batch.
{% endstep %}

{% step %}
Capture accession details such as identifiers, source, condition, and receiving time.
{% endstep %}

{% step %}
Link received items to project context and create or associate corresponding NGS sample records.
{% endstep %}

{% step %}
Verify traceability fields before moving materials into extraction workflows.
{% endstep %}
{% endstepper %}

### Extraction to Library Progression

Use this workflow to move materials through extraction and library preparation while preserving lineage.

{% stepper %}
{% step %}
Create or open an NGS sample record in `ngs_sample`.
{% endstep %}

{% step %}
Generate linked extraction records in `ngs_extract` and record extraction-specific metadata.
{% endstep %}

{% step %}
Create library records in `ngs_library` from eligible extracts.
{% endstep %}

{% step %}
Review parent-child links between sample, extract, and library records to confirm continuity.
{% endstep %}
{% endstepper %}

### FASTQ Registration and Experiment Documentation

Use this workflow to connect sequencing outputs with experiments and protocols.

{% stepper %}
{% step %}
Create FASTQ output records in `ngs_fastq` and attach output metadata.
{% endstep %}

{% step %}
Document run context in `eln_experiment` and link associated materials.
{% endstep %}

{% step %}
Associate the applied SOP or protocol from `eln_protocol`.
{% endstep %}

{% step %}
Store resulting files and related artifacts in designated storage records for downstream analysis and retrieval.
{% endstep %}
{% endstepper %}

### Storage and Consumption Control

Use this workflow to maintain inventory location history and material usage events.

{% stepper %}
{% step %}
Record material storage assignments and status updates in `core_storage`.
{% endstep %}

{% step %}
Log material usage events in `core_consumption` during extraction, library prep, and sequencing activities.
{% endstep %}

{% step %}
Review availability and usage history before launching additional workflows.
{% endstep %}
{% endstepper %}

## Advanced Features

### Visual Workflow Execution

Labii process workflows can convert complex NGS procedures into guided, visualized execution paths to reduce coordination overhead.

{% hint style="info" %}
Use process-driven execution when multiple users or handoff stages are involved to improve consistency and traceability.
{% endhint %}

### One-Click Material Progression

In configured sections, **Execute Workflow** can automate transitions and record updates for material consumption and downstream material creation.

{% hint style="success" %}
This approach is useful for high-throughput environments where manual status updates can introduce delays or errors.
{% endhint %}

### SOP-Centric Experiment Governance

By linking experiments to protocols, teams can enforce procedural alignment and improve reproducibility across projects.

## Troubleshooting

### Issue: LIMS for NGS template is not visible

**Symptoms**: You cannot find **LIMS for NGS** in template selection.

{% stepper %}
{% step %}
Confirm you are in **Settings** → **Applications** and selected **Add from a template**.
{% endstep %}

{% step %}
Check whether the application is already installed in your organization.
{% endstep %}

{% step %}
If still unavailable, contact your Labii administrator or Labii support to verify template availability for your account.
{% endstep %}
{% endstepper %}

### Issue: Missing lineage between sample, extract, and library

**Symptoms**: Downstream records are present but upstream links are incomplete.

{% stepper %}
{% step %}
Open the affected records and review linkage fields between `ngs_sample`, `ngs_extract`, and `ngs_library`.
{% endstep %}

{% step %}
Update missing relationships and save records.
{% endstep %}

{% step %}
Re-run workflow actions where needed so generated records inherit proper parent references.
{% endstep %}
{% endstepper %}

### Issue: Workflow automation does not progress as expected

**Symptoms**: **Execute Workflow** does not update the expected next stage.

{% stepper %}
{% step %}
Verify required fields are populated in the current record.
{% endstep %}

{% step %}
Confirm workflow steps are correctly configured in your organization settings.
{% endstep %}

{% step %}
Test with a new record to isolate whether the issue is configuration-specific or record-specific.
{% endstep %}
{% endstepper %}

## Related Documentation

* [Laboratory Information Management System](https://docs.labii.com/applications/laboratory-information-management-system)